Contacts of the helix formed by residues 100 - 118 (chain B) in PDB entry 3IKM
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 GLY 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.1 15.7 - - - +
80B SER* 2.9 21.4 - - - +
99B PHE* 1.3 73.0 - - - +
101B PRO* 1.3 81.0 - - - +
103B GLY* 3.2 11.4 + - - -
104B VAL* 3.5 6.4 + - - +
128C VAL* 3.1 12.9 - - - +
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Residues in contact with PRO 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG 4.6 2.2 - - - +
77B HIS* 3.2 31.2 - - + +
79B LEU 4.0 5.2 - - - +
80B SER* 4.4 2.5 - - - +
100B GLY* 1.3 88.6 - - - +
102B LEU* 1.3 67.1 + - + +
103B GLY 2.9 3.6 + - - -
104B VAL* 3.2 8.5 + - - +
105B GLU 4.2 1.4 + - - -
126C PHE* 4.5 7.9 - - + -
128C VAL* 2.8 28.0 - - + +
192C HIS* 4.7 5.8 - - + +
195C ASN* 5.0 10.1 - - + -
196C CYS* 5.3 12.1 - - - +
199C LEU* 4.4 15.9 - - + -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG 4.6 4.0 - - - +
76B ARG 3.7 8.3 - - - +
77B HIS 3.2 23.3 - - - +
78B PHE* 3.0 45.2 - - + +
100B GLY 3.9 0.2 - - - -
101B PRO* 1.3 83.3 - - + +
103B GLY* 1.3 61.5 + - - +
104B VAL 3.3 0.4 + - - -
105B GLU* 3.6 4.5 + - - +
106B LEU 3.5 2.6 + - - -
380B PRO* 3.1 31.8 - - + +
381B ILE* 5.6 7.2 - - + -
435B MET* 3.8 45.8 - - + +
126C PHE* 6.2 0.9 - - - -
199C LEU* 4.8 4.7 - - + -
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 2.8 26.4 - - - -
79B LEU* 5.9 0.2 - - - -
99B PHE* 6.5 0.4 - - - -
100B GLY 3.2 7.6 + - - -
101B PRO 2.9 4.8 + - - -
102B LEU* 1.3 76.2 - - - +
104B VAL* 1.3 49.9 + - - -
106B LEU* 2.8 9.4 - - - +
107B ARG 2.7 29.8 + - - -
346B MET* 3.2 19.4 - - - +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 5.4 6.5 - - + +
100B GLY 3.5 3.8 + - - +
101B PRO 3.2 6.0 + - - +
103B GLY* 1.3 71.0 - - - +
105B GLU* 1.3 71.7 + - - +
107B ARG* 2.6 17.2 + - + +
108B LYS* 2.5 34.8 + - + +
346B MET* 4.4 0.2 - - - +
126C PHE* 4.4 11.7 - - + -
128C VAL* 2.5 52.7 - - + +
129C ASP* 4.6 1.3 - - - +
210C GLN* 4.0 28.3 - - + +
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PRO 4.2 1.8 + - - -
102B LEU* 3.6 5.5 + - - +
103B GLY 3.4 0.4 - - - -
104B VAL* 1.3 78.9 - - - +
106B LEU* 1.3 54.1 + - - +
108B LYS* 3.5 10.9 - - - +
109B ASN* 2.5 56.1 + - - +
378B LEU 3.5 1.4 - - - +
380B PRO* 2.5 60.2 - - + +
381B ILE* 4.9 4.0 - - + -
382B LYS* 5.5 2.2 + - - -
412B SER* 5.7 2.0 - - - -
126C PHE* 5.0 19.5 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 4.8 11.4 - - + -
102B LEU 3.9 0.4 - - - +
103B GLY* 2.8 13.8 + - - +
105B GLU* 1.3 81.9 + - - +
107B ARG* 1.3 48.3 + - - +
109B ASN* 2.6 40.7 + - - +
110B LEU* 2.3 40.2 + - + +
346B MET* 3.6 38.1 - - + +
349B TYR* 5.8 4.0 - - + -
350B LEU* 6.0 4.3 - - + +
374B LEU* 5.9 7.2 - - + -
378B LEU* 3.8 25.6 - - + +
380B PRO* 3.4 19.0 - - + +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 3.6 18.4 - - - +
103B GLY 2.7 6.4 + - - +
104B VAL* 2.6 21.2 + - + +
106B LEU* 1.3 66.3 - - - +
108B LYS* 1.3 69.5 + - - +
109B ASN 2.8 1.1 - - - -
110B LEU* 2.8 13.9 + - - +
111B ALA* 2.9 20.2 + - + +
213B VAL* 6.0 1.4 - - - +
235B THR* 3.3 33.1 - - - +
342B LEU* 4.0 15.9 - - + -
343B ASP* 4.5 1.3 + - - +
346B MET* 3.4 37.1 - - + +
128C VAL 5.4 2.7 + - - -
129C ASP* 2.7 43.4 + - - -
130C ALA* 4.6 3.6 + - - +
131C LEU* 5.6 0.6 - - - +
210C GLN* 5.3 7.8 - - - +
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 2.5 25.4 + - + +
105B GLU* 3.7 10.8 - - - +
107B ARG* 1.3 76.9 - - - +
109B ASN* 1.3 57.3 + - - +
111B ALA* 4.4 3.7 - - - +
112B ALA* 3.0 29.4 + - + +
115C TRP* 3.5 53.1 - - + +
126C PHE* 6.3 0.2 - - + -
210C GLN* 3.7 21.4 + - - +
211C ILE* 5.9 0.8 - - - +
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Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLU* 2.5 34.6 + - - +
106B LEU* 2.6 43.3 + - - +
108B LYS* 1.3 74.0 - - - +
110B LEU* 1.3 69.6 + - - +
112B ALA* 3.6 3.9 - - - +
113B GLU* 3.2 28.1 + - - +
377B CYS 3.1 19.0 - - - +
378B LEU* 3.0 25.6 + - - +
382B LYS* 5.1 0.8 + - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 2.3 30.5 + - + +
107B ARG* 2.8 6.9 + - - +
109B ASN* 1.3 71.0 - - - +
111B ALA* 1.3 72.7 + - - +
113B GLU* 2.7 20.9 + - + +
114B TRP 3.2 5.5 + - - -
262B TRP* 3.5 31.4 - - + -
263B TRP* 4.7 9.2 - - + +
265B LYS* 6.2 0.9 - - - -
342B LEU* 3.1 36.8 - - + -
345B GLY 4.1 3.6 - - - +
346B MET* 3.9 31.9 - - + +
349B TYR* 5.3 10.1 - - + -
378B LEU* 6.0 6.3 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 2.9 17.3 + - + +
108B LYS* 4.4 3.8 - - - +
110B LEU* 1.3 77.9 - - - +
112B ALA* 1.3 53.8 + - - +
114B TRP* 2.6 38.5 + - - +
115B TRP* 2.9 5.6 + - + +
211B ILE* 3.6 34.5 - - + +
342B LEU* 5.1 9.6 - - + +
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Residues in contact with ALA 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 LYS* 3.0 21.9 + - + +
109B ASN* 3.6 6.1 - - - +
110B LEU 2.9 0.6 + - - -
111B ALA* 1.3 78.2 - - - +
113B GLU* 1.3 57.4 + - - +
115B TRP* 2.6 43.0 + - + +
116B THR* 3.1 6.0 + - - -
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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
----------------------------------------------------------
109B ASN* 3.2 20.4 + - - +
110B LEU* 2.7 16.0 + - + +
112B ALA* 1.3 76.8 - - - +
114B TRP* 1.3 51.8 + - - +
116B THR* 3.1 19.7 + - - +
117B SER 2.9 17.3 + - - -
262B TRP* 2.7 25.0 + - + -
265B LYS* 4.7 16.8 - - - +
377B CYS* 4.7 13.0 - - + +
378B LEU* 6.0 3.4 - - + -
483B LYS* 3.0 32.1 + - + +
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Residues in contact with TRP 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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110B LEU 4.2 0.2 - - - +
111B ALA* 2.6 22.6 + - - +
113B GLU* 1.3 66.9 - - - +
115B TRP* 1.3 56.4 + - - +
116B THR 2.7 8.7 + - - -
117B SER* 2.6 27.1 + - - -
118B VAL* 3.1 31.5 + - + -
119B VAL* 3.8 5.7 + - + -
209B ALA* 4.2 18.4 - - + -
211B ILE* 4.4 17.7 - - + -
237B ALA* 4.7 14.8 - - + -
238B SER 4.5 10.5 - - - -
239B LEU* 4.0 23.3 - - + -
259B ARG* 2.4 50.8 - - - +
262B TRP* 2.7 51.1 - + + -
263B TRP* 4.6 8.2 - + - -
301B GLU* 5.1 0.2 - - - -
338B VAL 4.9 3.1 - - - -
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Residues in contact with TRP 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 ALA* 2.9 5.3 + - + +
112B ALA* 2.6 27.3 + - - +
114B TRP* 1.3 78.8 - - - +
116B THR* 1.3 46.5 + - - -
119B VAL* 2.6 49.7 - - + +
120B VAL* 2.6 31.1 + - + +
127B PRO* 4.5 24.5 - - + -
210B GLN* 6.5 0.2 - - - -
211B ILE* 4.6 24.9 - - + +
104C VAL* 4.7 6.7 - - + -
105C GLU* 4.6 4.2 + - - -
108C LYS* 3.0 53.2 - - + +
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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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112B ALA 3.1 8.2 + - - -
113B GLU* 3.2 23.7 + - - +
114B TRP 2.7 2.8 + - - -
115B TRP* 1.3 77.0 - - - +
117B SER* 1.3 59.5 + - - -
118B VAL 2.7 0.3 + - - -
119B VAL 3.1 0.2 + - - -
120B VAL* 2.7 45.0 + - + +
121B PHE* 2.6 38.8 - - + -
483B LYS* 6.5 0.9 - - + -
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLU 2.9 7.3 + - - -
114B TRP* 2.6 16.9 + - - -
116B THR* 1.3 70.4 - - - +
118B VAL* 1.3 60.7 + - - -
121B PHE* 3.0 25.8 - - - +
258B HIS* 3.1 17.5 + - - -
259B ARG* 2.9 21.2 + - - +
262B TRP* 2.4 51.4 + - - +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TRP* 3.5 48.0 - - + -
116B THR 2.7 2.8 + - - +
117B SER* 1.3 77.7 - - - +
119B VAL* 1.3 78.9 + - + +
120B VAL 3.5 0.2 + - - -
121B PHE* 3.8 10.9 + - - +
122B ARG* 4.1 14.0 + - + +
125B VAL* 5.1 12.6 - - + +
209B ALA* 5.4 0.2 - - + -
239B LEU* 3.7 28.3 - - + -
241B TRP* 5.9 2.0 - - + -
255B TRP* 5.8 3.4 - - + -
258B HIS* 4.0 17.5 - - + +
259B ARG* 4.8 1.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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