Contacts of the strand formed by residues 40 - 52 (chain A) in PDB entry 1I1B
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A THR* 3.8 14.0 - - - +
10A LEU 5.1 0.5 + - - -
18A LEU* 3.0 12.2 + - + +
19A VAL* 3.5 9.2 - - - +
20A MET* 3.5 42.0 - - + +
26A LEU* 4.6 5.4 - - + -
38A GLN 4.9 1.1 - - - +
39A GLN* 1.3 75.4 - - - +
41A VAL* 1.3 64.8 + - - +
42A PHE* 4.0 28.1 + - + -
62A LEU* 3.7 33.4 - - + -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ASN* 3.9 2.9 - - + -
8A CYS 3.6 5.4 - - - +
9A THR* 3.9 17.7 - - + -
39A GLN* 3.6 8.2 + - + +
40A VAL* 1.3 74.2 - - - +
42A PHE* 1.3 70.1 + - - +
62A LEU* 3.8 4.3 - - - +
63A LYS* 2.9 55.9 + - + +
151A VAL* 3.8 27.4 - - + -
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ASN* 3.2 7.8 - - - +
8A CYS* 2.9 48.4 + - - +
10A LEU* 4.1 32.8 - - + -
18A LEU* 4.2 17.9 - - + -
26A LEU* 4.1 16.4 - - + -
40A VAL* 4.0 25.1 - - + -
41A VAL* 1.3 78.6 - - - +
43A SER* 1.3 64.6 - - - +
44A MET 3.8 0.7 - - - +
60A LEU* 4.2 22.4 - - + -
61A GLY 3.1 16.4 - - - +
62A LEU* 3.8 18.6 - - + -
63A LYS* 4.1 2.2 - - - -
69A LEU* 4.0 22.7 - - + -
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 3.6 22.9 + - - -
6A LEU 3.6 4.3 - - - -
7A ASN* 3.9 12.1 + - - -
42A PHE* 1.3 74.3 - - - +
44A MET* 1.3 58.8 + - - +
45A SER* 3.6 7.0 + - - -
59A ALA 3.7 0.5 - - - +
61A GLY* 2.8 35.3 + - - -
62A LEU 4.7 1.6 - - - -
63A LYS* 4.0 14.3 - - - +
68A TYR* 5.3 4.1 - - - -
91A PRO* 6.0 0.9 - - - +
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Residues in contact with MET 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 3.2 2.8 - - - -
6A LEU* 2.8 48.6 + - + +
8A CYS* 4.2 15.5 - - - -
10A LEU* 5.1 1.6 - - + -
42A PHE 3.8 1.6 - - - -
43A SER* 1.3 69.6 - - - +
45A SER* 1.3 59.4 + - - +
46A PHE* 3.8 16.7 - - + -
58A VAL* 3.8 30.7 - - + -
59A ALA 3.4 4.9 - - - -
60A LEU* 3.9 17.5 - - + -
103A LYS* 4.0 11.4 - - + -
112A PHE* 3.9 32.5 - - + -
148A MET* 3.9 23.3 - - - +
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 4.3 7.9 - - - -
4A ARG 3.4 7.0 - - - -
5A SER* 2.9 19.2 + - - -
43A SER* 3.6 6.1 + - - -
44A MET* 1.3 71.7 - - - +
46A PHE* 1.3 62.5 + - - +
47A VAL* 3.4 14.5 + - - -
58A VAL* 3.1 9.6 - - - +
59A ALA* 2.9 38.7 + - - -
68A TYR* 5.3 3.0 + - - -
91A PRO* 3.8 21.8 - - - +
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.2 16.9 - - - +
4A ARG* 2.9 39.4 + - + +
5A SER 4.7 1.8 - - - -
6A LEU* 3.8 33.4 - - + -
44A MET* 3.8 24.5 - - + -
45A SER* 1.3 70.0 - - - +
47A VAL* 1.3 63.0 + - - +
56A ILE* 3.8 27.4 - - + -
57A PRO 3.9 2.9 - - - +
58A VAL* 3.8 15.5 - - + -
93A LYS* 5.1 0.9 - - - +
103A LYS* 4.3 10.3 - - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 4.5 0.7 - - + -
45A SER* 3.4 11.2 + - - +
46A PHE* 1.3 78.1 - - - +
48A GLN* 1.3 73.3 + - - +
57A PRO* 3.4 35.5 + - + +
58A VAL 4.1 4.5 - - - -
59A ALA* 3.8 24.7 - - + -
92A LYS 3.8 19.3 - - - +
93A LYS* 3.3 14.1 - - - +
95A MET* 3.9 7.9 - - + -
100A VAL* 3.9 24.2 - - + -
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A VAL* 1.3 86.9 - - - +
49A GLY* 1.3 63.8 + - - +
57A PRO* 4.3 2.9 - - - +
93A LYS* 2.8 23.2 + - + +
94A LYS* 3.8 22.5 - - - +
95A MET 5.4 2.9 + - - +
100A VAL* 4.8 6.6 - - - +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A VAL 4.0 1.2 + - - -
48A GLN* 1.3 83.6 - - - +
50A GLU* 1.3 63.0 + - - -
51A GLU* 3.7 4.7 + - - +
57A PRO* 4.0 13.4 - - - +
100A VAL* 5.8 1.8 - - - -
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLY* 1.3 71.8 - - - -
51A GLU* 1.3 58.5 + - - +
55A LYS* 4.1 8.8 - - - +
57A PRO* 4.0 13.0 - - - +
97A LYS* 4.8 10.9 + - - -
102A ASN* 4.4 13.3 + - - +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLY 3.7 5.0 + - - +
50A GLU* 1.3 73.3 - - - +
52A SER* 1.3 74.2 + - - +
53A ASN* 5.6 0.2 - - - -
55A LYS 3.2 11.4 - - - +
56A ILE* 4.2 17.7 - - - +
57A PRO* 3.8 14.6 - - + +
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 1.3 88.9 - - - +
53A ASN* 1.3 76.7 + - - +
54A ASP* 3.1 13.0 + - - +
55A LYS* 2.8 31.1 + - - +
56A ILE* 3.7 4.7 - - - +
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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