Contacts of the helix formed by residues 108 - 127 (chain B) in PDB entry 3RCH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLY 4.2 2.5 - - - -
68A VAL* 4.6 8.5 - - - +
69A THR* 4.8 5.5 + - - -
107B ALA* 1.3 83.1 + - - +
109B PRO* 1.4 65.2 - - - +
110B ALA 3.3 2.2 - - - -
111B CYS* 3.4 11.0 + - - +
112B THR* 3.3 25.2 + - - -
357B PHE* 3.2 38.8 - - - -
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO* 4.0 14.1 - - + -
33A VAL* 4.0 27.8 - - + -
37A TYR* 4.7 6.1 - - + -
67A GLY 3.3 12.8 - - - +
107B ALA* 3.5 9.6 - - - +
108B SER* 1.4 85.0 - - - +
110B ALA* 1.3 64.0 + - - +
112B THR* 3.5 5.0 + - - +
113B GLU* 3.1 36.1 + - + +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 3.3 24.2 + - - +
38A LEU* 4.0 9.1 - - + +
64A ILE* 3.7 30.1 - - + +
67A GLY 3.0 23.0 + - - +
68A VAL* 4.2 3.8 - - + -
109B PRO* 1.3 77.9 - - - +
111B CYS* 1.3 57.6 + - - +
114B LEU* 3.1 32.7 + - - +
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Residues in contact with CYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 5.7 5.2 - - - -
68A VAL* 4.6 8.3 - - - -
108B SER* 3.4 14.4 + - - +
109B PRO 3.3 0.6 - - - -
110B ALA* 1.3 78.6 - - - +
112B THR* 1.3 65.1 + - - +
114B LEU* 4.7 1.3 - - - -
115B GLU* 3.4 16.6 + - - +
357B PHE* 3.0 63.9 - - + -
359B SER* 3.4 22.4 + - - +
360B LEU* 5.7 6.7 - - - -
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER 3.3 14.5 + - - -
109B PRO* 3.9 8.2 - - - +
111B CYS* 1.3 77.4 - - - +
113B GLU* 1.3 66.5 + - + +
115B GLU* 3.4 18.4 - - - +
116B THR* 3.2 17.3 + - - +
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.6 7.4 - - - +
36A GLY* 2.7 34.5 + - - -
37A TYR* 4.1 8.5 + - - -
38A LEU* 3.2 41.6 + - + +
39A ARG* 4.1 3.3 + - + +
109B PRO* 3.1 22.3 + - + +
110B ALA 4.3 0.4 - - - +
112B THR* 1.3 80.0 - - + +
114B LEU* 1.3 64.8 + - - +
116B THR* 3.3 11.7 + - - -
117B VAL* 3.2 24.4 + - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.4 9.1 - - + +
42A ILE* 3.6 28.7 - - + -
64A ILE* 3.8 24.0 - - + -
110B ALA 3.1 19.0 + - - +
111B CYS* 5.8 1.1 - - - -
113B GLU* 1.3 76.6 - - - +
115B GLU* 1.3 56.9 + - - +
117B VAL* 3.1 3.1 + - + -
118B MET* 2.8 54.7 + - + +
359B SER* 3.7 24.0 - - - +
360B LEU* 3.8 25.1 - - + +
363B TRP* 3.8 13.7 - - + -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B CYS 3.4 13.7 + - - +
112B THR* 3.4 14.6 + - - +
113B GLU 3.2 0.2 - - - -
114B LEU* 1.3 79.3 - - - +
116B THR* 1.3 56.3 + - - +
118B MET* 3.4 3.6 + - - +
119B MET* 2.9 37.5 + - + +
143B VAL* 5.1 4.2 - - - +
144B ILE* 3.6 40.8 + - + +
358B ARG* 3.4 29.0 + - - +
359B SER* 3.4 15.5 + - - +
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 3.3 21.1 - - - +
112B THR* 3.2 15.4 + - - +
113B GLU* 3.3 11.4 + - - -
114B LEU 3.3 0.4 - - - -
115B GLU* 1.3 76.8 - - - +
117B VAL* 1.3 62.3 + - - +
119B MET* 3.4 7.3 + - - +
120B ASP* 3.2 21.7 + - - +
134B ASN* 3.3 32.1 + - + +
142B GLY 5.9 2.0 - - - -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.4 5.6 - - + -
39A ARG* 3.9 51.1 - - + +
42A ILE* 3.7 28.9 - - + +
43A PRO 4.4 3.1 - - - +
44A ALA* 5.6 0.7 - - - +
113B GLU 3.2 12.8 + - - +
114B LEU* 3.1 9.7 + - + +
116B THR* 1.3 75.4 - - - +
118B MET* 1.3 66.2 + - + +
120B ASP* 3.2 9.3 + - + +
121B TRP* 2.9 35.6 + - + +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 4.5 0.7 - - + -
114B LEU* 2.8 35.6 + - + +
115B GLU* 3.7 6.3 - - - +
117B VAL* 1.3 80.8 - - + +
119B MET* 1.3 61.6 + - + +
121B TRP* 3.0 36.3 + - + +
122B LEU* 2.9 30.2 + - - +
359B SER* 3.8 20.4 - - - +
362B MET* 4.0 25.5 - - + +
363B TRP* 3.5 45.5 - - + +
366B PHE* 4.3 5.4 - - - -
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU* 2.9 23.4 + - + +
116B THR* 3.6 7.6 - - - +
117B VAL 3.3 0.2 - - - -
118B MET* 1.3 76.4 - - - +
120B ASP* 1.3 57.4 + - - +
122B LEU* 3.6 7.4 + - - -
123B GLY* 3.0 23.9 + - - -
134B ASN* 6.1 2.9 - - + -
142B GLY* 4.1 17.5 - - - +
143B VAL* 3.7 23.8 - - - +
144B ILE* 3.6 32.3 - - + +
313B ALA* 3.6 21.8 - - + -
314B MET 4.0 1.8 - - - +
315B TRP* 3.3 49.7 + - + +
362B MET* 5.4 1.8 - - - +
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 2.9 38.5 + - - +
44A ALA 5.1 1.8 - - - +
116B THR 3.2 7.9 + - - +
117B VAL* 3.2 10.9 + - + +
118B MET 3.1 0.6 - - - -
119B MET* 1.3 76.3 - - - +
121B TRP* 1.3 67.6 + - + +
123B GLY* 3.1 2.8 + - - -
124B LYS* 2.9 33.0 + - - +
133B LEU* 4.4 6.0 - - - +
134B ASN* 3.4 14.9 + - - +
135B GLU* 3.4 41.1 + - + +
315B TRP* 5.9 0.7 + - - -
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Residues in contact with TRP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 4.0 11.9 - - + -
43A PRO* 3.0 29.7 + - + -
44A ALA 3.4 16.6 - - - -
45A ALA* 3.0 29.8 - - - +
46A ALA* 3.4 22.8 + - + +
47A PRO* 3.9 19.1 - - + -
51A ASP* 5.7 0.2 - - - -
117B VAL* 2.9 21.4 + - + +
118B MET* 3.3 33.7 - - + +
120B ASP* 1.3 76.1 - - - +
122B LEU* 1.3 62.4 + - - +
124B LYS* 3.2 7.6 + - - +
125B MET* 3.0 34.0 + - + +
363B TRP* 4.0 22.4 - + - -
366B PHE* 3.9 20.9 - + + -
367B ARG* 4.0 11.0 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B MET 2.9 13.0 + - - +
119B MET* 3.9 8.1 - - - +
121B TRP* 1.3 74.9 - - - +
123B GLY* 1.3 65.5 - - - +
125B MET* 3.0 16.7 + - + +
126B LEU* 3.0 28.3 + - + +
280B ILE* 5.5 0.2 - - + -
299B PHE* 3.8 20.4 - - + -
301B PRO* 4.0 23.3 - - + -
305B LEU* 3.6 31.0 - - + -
313B ALA* 4.3 13.5 - - + -
315B TRP* 4.2 4.9 - - + -
362B MET* 3.7 25.4 - - + -
366B PHE* 3.9 10.3 - - + -
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B MET 3.0 13.6 + - - -
120B ASP* 3.4 4.9 - - - -
121B TRP 3.1 0.2 - - - -
122B LEU* 1.3 82.7 - - - +
124B LYS* 1.3 55.6 + - - +
126B LEU* 3.2 2.5 + - - +
127B GLU 2.9 21.7 + - - -
128B LEU* 3.6 20.1 + - - +
133B LEU* 5.9 8.5 - - - -
315B TRP* 3.9 15.8 - - - -
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 3.1 39.4 + - - +
45A ALA* 4.2 17.4 - - + +
120B ASP* 2.9 22.8 + - - +
121B TRP* 3.9 4.9 - - - +
123B GLY* 1.3 74.9 - - - +
125B MET* 1.3 63.5 + - - +
127B GLU* 3.0 26.7 + - - +
133B LEU* 5.3 11.2 - - + -
135B GLU* 2.8 39.8 + - - +
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Residues in contact with MET 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 3.7 22.9 - - + -
121B TRP* 3.0 24.6 + - + +
122B LEU* 3.0 23.8 + - + +
124B LYS* 1.3 79.4 - - - +
126B LEU* 1.3 60.1 + - - +
127B GLU* 4.1 0.3 - - - +
280B ILE* 3.5 41.0 - - + +
285B ARG* 3.7 13.0 + - - -
305B LEU* 4.7 1.6 - - - -
366B PHE* 4.0 26.2 - - + -
371B VAL* 3.8 31.4 - - + -
374B LEU* 4.3 16.8 - - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU* 3.0 16.6 + - + +
123B GLY 3.8 2.2 - - - +
125B MET* 1.3 72.9 - - - +
127B GLU* 1.3 73.6 + - - +
128B LEU* 3.7 24.0 - - + -
276B GLY 3.0 30.3 - - - +
277B SER* 4.6 1.1 - - - -
279B PHE* 4.0 25.2 - - + +
280B ILE* 4.1 16.2 - - + -
285B ARG* 4.0 3.8 + - - -
288B LEU* 4.0 12.6 - - + +
297B PHE* 4.2 4.3 - - + -
299B PHE* 3.3 35.7 - - + -
315B TRP* 4.1 13.9 - - + -
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLY 2.9 6.9 + - - -
124B LYS* 3.0 21.2 + - - +
125B MET 4.1 2.9 - - - +
126B LEU* 1.3 84.2 - - - +
128B LEU* 1.3 66.0 + - - +
129B PRO* 4.6 1.0 - - - +
285B ARG* 4.0 33.5 + - - +
288B LEU* 4.5 6.6 - - - +
291B VAL* 5.9 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il