Contacts of the strand formed by residues 35 - 42 (chain A) in PDB entry 5DPT
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 ARG 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ILE* 6.1 0.4 - - - -
29A ARG* 2.8 22.9 + - - -
32A TYR* 3.3 28.7 + - + +
33A PRO 3.3 0.6 - - - -
34A ASP* 1.3 109.7 + - - +
36A VAL* 1.3 66.1 + - - +
37A PRO* 4.1 1.6 - - - +
57A LEU* 4.7 22.5 + - + +
58A VAL 3.2 13.2 - - - +
59A PRO* 4.2 25.2 - - + +
60A SER 4.1 0.4 - - - +
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Residues in contact with VAL 36 (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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29A ARG* 4.0 11.0 - - - +
35A ARG* 1.3 80.4 - - - +
37A PRO* 1.3 65.4 - - - +
38A VAL* 3.5 21.1 + - + -
56A TYR 3.4 2.1 - - - +
57A LEU* 3.5 4.2 - - - -
58A VAL* 2.5 44.9 + - + +
60A SER* 4.6 9.6 - - - -
98A MET* 4.2 13.2 - - + +
99A GLY* 4.6 9.0 - - - -
102A TYR* 3.4 46.9 - - + -
112A LEU* 4.6 1.3 - - + -
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Residues in contact with PRO 37 (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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25A GLY 5.1 0.7 - - - +
28A ILE* 4.4 19.1 - - + -
29A ARG* 4.0 22.0 - - + +
35A ARG 4.1 1.8 - - - +
36A VAL* 1.3 88.2 - - + +
38A VAL* 1.3 61.1 + - - +
39A ILE* 5.6 0.2 - - - -
56A TYR 3.4 6.3 - - - +
57A LEU* 4.0 13.6 - - + -
102A TYR* 4.3 3.5 - - + +
110A TYR 3.4 22.9 - - - +
111A PHE* 3.6 26.7 - - + -
112A LEU 3.2 20.3 + - - -
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Residues in contact with VAL 38 (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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36A VAL* 3.7 23.1 - - + +
37A PRO* 1.3 79.1 - - - +
39A ILE* 1.3 68.0 + - - +
40A VAL* 3.7 22.1 + - + -
54A ARG 3.5 2.4 - - - +
55A LYS 3.9 0.2 - - - -
56A TYR* 2.7 41.9 + - + +
58A VAL* 4.2 10.5 - - + -
67A PHE* 4.2 7.4 - - + -
98A MET* 3.7 20.6 - - + -
112A LEU* 3.3 15.3 - - + +
114A VAL* 3.8 19.7 - - + -
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Residues in contact with ILE 39 (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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10A PHE* 4.7 1.3 - - + -
12A TYR* 3.9 40.2 - - + -
37A PRO* 6.2 0.2 - - + -
38A VAL* 1.3 77.7 - - - +
40A VAL* 1.3 59.9 + - - +
41A GLU* 4.0 16.4 - - + +
54A ARG* 3.5 8.5 - - + +
55A LYS* 4.0 25.1 - - + -
111A PHE* 4.3 22.2 - - + -
112A LEU 2.7 11.2 + - - +
113A TYR* 3.5 35.9 - - + +
114A VAL* 2.7 32.6 + - - +
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Residues in contact with VAL 40 (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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38A VAL* 3.7 20.6 - - + -
39A ILE* 1.3 75.0 - - - +
41A GLU* 1.3 64.4 + - - +
51A LEU* 3.8 26.5 - - + +
54A ARG* 3.0 30.3 + - - +
56A TYR* 3.8 19.3 - - + -
67A PHE* 3.9 17.0 - - + -
71A ILE* 4.4 11.0 - - + -
85A PHE* 5.0 1.3 - - + -
114A VAL* 3.2 16.6 - - + +
116A TYR* 3.8 22.6 - - + -
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Residues in contact with GLU 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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10A PHE* 3.8 24.3 - - + +
11A GLN* 2.8 33.2 + - - +
12A TYR* 2.8 32.2 + - - +
39A ILE* 4.0 7.2 + - + +
40A VAL* 1.3 79.3 - - - +
42A LYS* 1.3 67.4 + - - +
50A ASP* 5.8 0.7 - - - -
51A LEU* 5.9 0.7 - - - -
54A ARG* 2.9 21.4 + - + +
114A VAL 3.0 6.7 + - - -
115A ALA* 3.2 7.5 - - - -
116A TYR* 3.1 32.0 + - - -
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Residues in contact with LYS 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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41A GLU* 1.3 80.7 - - - +
43A ALA* 1.3 75.9 - - - +
44A PRO* 3.7 4.2 - - - +
46A ALA* 3.9 17.5 - - + +
48A VAL* 3.2 41.3 - - + +
50A ASP* 4.1 22.7 + - + +
115A ALA* 5.2 0.9 - - - -
116A TYR* 3.4 24.9 + - + +
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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