Contacts of the strand formed by residues 30 - 37 (chain A) in PDB entry 5AVD
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 GLN 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A TRP* 3.0 25.6 + - + +
28A PRO 4.5 3.8 - - - +
29A SER* 1.3 80.4 + - - +
31A ILE* 1.3 83.8 + - - +
46A GLY* 3.7 16.6 - - - -
47A GLY 3.6 7.7 + - - +
71A VAL 4.6 1.7 - - - +
72A VAL* 5.5 0.2 - - - +
73A GLY 4.7 9.2 + - - -
74A GLU 5.1 3.3 + - - +
123A TYR 5.7 0.2 - - - +
145A THR* 2.7 40.4 + - - +
146A GLY* 4.4 4.0 - - - -
147A TRP* 3.6 30.2 - - + -
160A LEU* 3.8 17.5 - - + -
205A GLY* 4.4 1.0 - - - -
206A PRO* 3.3 16.3 - - + +
208A HIS* 5.4 0.4 - - - -
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Residues in contact with ILE 31 (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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28A PRO 5.8 0.7 - - - +
29A SER 3.6 11.4 - - - +
30A GLN* 1.3 98.1 + - - +
32A SER* 1.4 75.2 + - - +
33A LEU* 3.5 13.7 - - + +
46A GLY* 3.4 2.9 - - - -
47A GLY* 2.9 45.7 + - - +
49A LEU* 4.0 13.7 - - + +
55A VAL* 3.7 20.9 - - + -
70A VAL* 3.9 14.8 - - + -
71A VAL 3.5 9.4 - - - +
72A VAL* 3.7 27.1 - - + -
147A TRP* 3.6 5.7 - - - -
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 1.4 74.3 - - - +
33A LEU* 1.3 60.5 + - - +
34A GLN* 2.9 29.8 + - - +
43A HIS* 2.8 24.8 + - - -
45A CYS 3.8 3.8 - - - -
69A ARG 3.8 0.5 - - - +
70A VAL* 3.4 4.0 - - - -
71A VAL* 2.9 40.5 + - - -
74A GLU* 4.8 1.6 - - - -
77A LEU* 3.8 6.4 - - - +
147A TRP* 3.8 18.3 - - - -
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Residues in contact with LEU 33 (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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31A ILE* 3.5 10.8 - - + +
32A SER* 1.3 70.7 - - - +
34A GLN* 1.3 60.7 + - - +
43A HIS* 3.8 0.7 - - - -
44A THR* 2.9 27.9 + - + +
45A CYS* 2.8 38.7 + - + +
46A GLY 4.4 1.8 - - - +
57A THR* 4.3 9.0 - - - +
61A CYS* 4.1 8.5 - - + -
62A VAL* 4.0 24.0 - - + -
68A PHE* 4.0 30.1 - - + -
69A ARG 3.6 15.0 - - - +
70A VAL* 4.1 5.8 - - + -
89A VAL* 4.3 0.2 - - + -
112A LEU* 3.8 26.0 - - + -
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Residues in contact with GLN 34 (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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32A SER* 2.9 34.3 + - - +
33A LEU* 1.3 73.8 - - - +
35A TYR* 1.3 61.2 + - - +
41A TRP* 3.6 9.1 - - + +
42A ALA 3.1 14.8 - - - +
43A HIS* 3.9 11.4 - - - +
44A THR* 4.3 0.7 - - - +
68A PHE* 3.2 10.0 - - - -
69A ARG* 2.9 73.7 + - + +
71A VAL* 3.5 20.7 - - + +
74A GLU* 5.1 2.6 + - - -
77A LEU* 3.8 16.6 - - - +
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Residues in contact with TYR 35 (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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34A GLN* 1.3 73.9 - - - +
36A ARG* 1.3 73.2 + - - +
37A SER* 2.6 31.5 + - - -
41A TRP* 3.4 7.8 - - - -
42A ALA* 2.9 52.4 + - + +
43A HIS 4.7 1.8 - - - -
44A THR* 3.8 27.1 - - + -
64A ARG* 4.3 17.7 + - - -
66A LEU* 3.7 37.9 - - + -
67A THR 3.2 10.1 - - - +
68A PHE* 4.2 5.6 - - + -
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Residues in contact with ARG 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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35A TYR* 1.3 81.2 - - - +
37A SER* 1.3 60.6 + - - +
38A GLY* 3.7 26.3 + - - +
39A SER* 5.6 1.1 - - - +
40A SER 3.6 9.0 - - - +
41A TRP* 3.5 29.5 - - + +
66A LEU* 5.4 4.0 - - - +
67A THR* 2.9 41.3 + - - +
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Residues in contact with SER 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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35A TYR* 2.6 41.8 + - - -
36A ARG* 1.3 71.1 - - - +
38A GLY* 1.3 58.8 + - - +
39A SER 3.3 0.3 + - - -
40A SER* 2.7 46.7 + - - -
42A ALA* 3.8 11.6 - - - +
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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