Contacts of the strand formed by residues 108 - 120 (chain B) in PDB entry 4OD9
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 VAL 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 4.4 10.5 - - + +
93A SER* 3.3 1.2 - - - -
94A VAL* 2.9 51.0 + - + +
97A GLN* 3.0 15.7 + - - +
107B GLY* 1.3 74.4 - - - +
109B LYS* 1.3 64.9 + - - +
110B VAL* 4.1 5.8 - - + -
154B LEU* 4.3 15.7 - - + -
159B LEU* 3.6 43.7 - - + +
160B VAL* 5.5 1.8 - - + -
183B LEU* 4.2 15.3 - - + -
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 5.1 2.2 + - - -
23A THR* 5.9 1.0 + - - -
25A PRO* 3.7 20.8 - - - +
91A THR* 4.1 18.1 - - + +
92A VAL 3.5 3.4 - - - -
93A SER* 2.8 33.1 + - - +
97A GLN* 4.1 19.6 + - - +
108B VAL* 1.3 76.7 - - - +
110B VAL* 1.3 63.2 - - - +
111B GLU* 3.5 9.9 + - + +
157B GLN* 4.2 1.0 - - - +
159B LEU* 3.4 17.9 - - - +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP 4.1 1.2 - - - +
91A THR* 3.4 2.5 - - - -
92A VAL* 2.8 48.4 + - + +
94A VAL* 5.6 1.8 - - + -
108B VAL* 4.5 9.2 - - + -
109B LYS* 1.3 71.3 - - - +
111B GLU* 1.3 62.2 + - - +
113B GLN* 3.8 10.4 - - + +
150B VAL* 4.1 18.2 - - + +
153B ASN* 3.6 37.7 - - + +
154B LEU* 4.1 35.9 - - + +
157B GLN* 4.1 2.0 - - - +
159B LEU* 4.0 7.6 - - + -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 4.2 17.0 + - + +
109B LYS* 3.5 8.5 + - + +
110B VAL* 1.3 71.5 - - - +
112B ARG* 1.3 96.2 + - + +
153B ASN* 3.0 6.9 + - - -
157B GLN* 2.8 39.2 + - - +
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Residues in contact with ARG 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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66A THR* 6.0 4.8 + - - +
68A VAL* 5.8 4.8 - - - +
89A GLN* 3.6 38.3 + - - +
90A ASP 3.8 9.6 + - - -
91A THR* 4.5 2.2 + - - -
111B GLU* 1.3 99.7 + - + +
113B GLN* 1.3 60.8 + - - +
114B VAL* 3.8 3.5 + - - +
153B ASN* 3.5 6.8 + - - +
157B GLN* 5.4 0.4 - - - +
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.4 5.0 - - + +
89A GLN* 3.3 3.4 - - - -
90A ASP 2.9 33.1 + - - +
92A VAL* 3.7 26.2 - - + -
110B VAL* 3.8 9.7 - - + +
111B GLU 3.2 0.4 + - - -
112B ARG* 1.3 76.5 - - - +
114B VAL* 1.3 83.2 + - - +
115B PHE* 3.6 4.7 - - + -
147B VAL* 4.5 0.4 - - - +
148B LEU 2.9 26.2 + - - -
149B PRO* 4.2 0.8 - - - +
150B VAL* 3.3 40.9 - - + +
153B ASN* 3.0 25.1 + - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.9 2.8 + - - +
70A ASN* 4.8 4.0 - - - +
87A LEU* 4.0 29.6 - - + -
88A SER 3.4 11.2 - - - +
89A GLN* 4.1 24.7 - - + +
112B ARG 3.8 3.3 + - - +
113B GLN* 1.3 96.5 + - - +
115B PHE* 1.3 62.6 + - - +
147B VAL* 3.4 30.5 - - + +
148B LEU 5.0 1.0 + - - +
1E NAG 4.1 18.4 - - - +
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Residues in contact with PHE 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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21A ILE* 3.6 38.6 - - + -
39A LEU* 3.4 35.7 - - + +
41A VAL* 4.2 12.6 - - + -
59A TYR* 3.7 26.5 - + - -
87A LEU* 3.5 9.7 - - - -
88A SER* 3.0 47.9 + - - +
89A GLN 4.0 0.2 - - - -
90A ASP* 3.8 20.2 - - + -
92A VAL* 5.2 1.8 - - + -
113B GLN* 3.6 13.9 - - + +
114B VAL* 1.3 75.8 - - - +
116B GLY* 1.3 71.2 + - - +
117B GLU* 4.0 18.6 - - + -
147B VAL* 5.3 0.9 - - - -
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Residues in contact with GLY 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 LEU 2.8 16.2 + - - -
40A TRP* 3.2 4.1 - - - +
41A VAL 3.0 27.5 + - - +
74A PHE* 3.4 26.5 - - - -
86A TYR 3.7 1.8 - - - -
87A LEU* 4.3 3.3 - - - +
115B PHE* 1.3 81.1 - - - +
117B GLU* 1.3 60.1 + - - -
118B ALA 3.7 0.9 - - - -
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Residues in contact with GLU 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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41A VAL 3.6 4.7 - - - -
43A SER* 2.7 34.5 + - - +
45A HIS* 4.2 2.8 + - - -
59A TYR* 3.3 41.5 - - + +
61A SER* 4.1 5.1 + - - -
67A TYR* 4.0 5.4 - - - -
74A PHE* 4.0 1.3 - - - -
85A GLY* 3.3 1.7 - - - -
86A TYR* 2.8 57.0 + - + +
88A SER* 2.6 28.5 + - - +
115B PHE* 4.0 10.0 + - + -
116B GLY* 1.3 69.7 - - - -
118B ALA* 1.4 64.0 + - - +
119B THR* 3.5 3.6 + - - +
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Residues in contact with ALA 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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40A TRP* 3.8 13.7 - - + -
41A VAL 2.8 19.5 + - - +
42A PRO* 3.8 5.1 - - + +
43A SER* 2.9 27.4 + - - +
46A CYS* 3.9 5.5 - - - +
50A ASP* 4.9 1.4 - - - +
74A PHE* 4.2 4.0 - - + -
83A LEU* 3.8 27.8 - - + -
84A SER 3.6 7.4 - - - +
116B GLY 3.7 1.8 + - - -
117B GLU* 1.4 69.1 - - - +
119B THR* 1.3 59.2 + - - +
121B GLN* 4.6 12.7 + - + -
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Residues in contact with THR 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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43A SER* 4.1 2.9 - - - -
45A HIS* 3.6 25.8 - - + +
46A CYS* 3.5 6.8 - - - +
47A LYS* 2.9 43.8 + - - +
50A ASP* 3.8 8.1 - - - +
84A SER 2.9 6.6 + - - -
85A GLY* 3.5 13.3 - - - -
86A TYR* 3.8 31.4 - - + -
117B GLU 3.5 4.7 + - - +
118B ALA* 1.3 77.3 - - - +
120B LYS* 1.3 68.6 + - - +
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Residues in contact with LYS 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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47A LYS* 3.8 33.9 - - + +
50A ASP* 4.0 3.6 - - - -
83A LEU* 3.3 4.5 - - - +
84A SER* 3.0 50.6 + - - +
119B THR* 1.3 88.3 - - - +
121B GLN* 1.3 66.8 + - - +
122B PRO* 3.8 8.5 - - + -
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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