Contacts of the strand formed by residues 30 - 41 (chain D) in PDB entry 6Q3W
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 LEU 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D PRO* 3.5 2.5 - - - +
29D GLU* 1.3 97.3 - - + +
31D ALA* 1.3 61.5 + - - +
32D VAL* 5.7 2.2 - - + -
64D VAL* 3.3 19.7 - - - +
65D GLY 3.1 21.2 + - - +
67D PRO* 5.2 7.9 - - + -
152D PHE* 3.8 29.6 - - + +
155D GLN* 3.9 36.6 - - + +
156D LEU* 4.2 16.8 - - + -
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.9 21.5 - - + -
30D LEU* 1.3 77.7 - - - +
32D VAL* 1.3 67.0 + - - +
62D VAL* 5.4 0.4 - - + -
63D LEU 3.6 6.1 - - - +
64D VAL* 3.8 13.9 - - + -
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 5.7 2.2 - - + -
31D ALA* 1.3 80.8 - - - +
33D SER* 1.3 65.5 + - - +
62D VAL* 3.3 10.2 - - - +
63D LEU* 3.2 43.0 + - + +
148D ALA* 3.3 27.6 - - - +
151D THR* 3.7 35.4 - - + +
152D PHE* 4.0 15.5 - - + -
155D GLN* 5.0 11.9 - - + +
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Residues in contact with SER 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 1.3 82.3 - - - +
34D ALA* 1.3 62.4 + - - +
60D MET* 3.7 27.6 - - - -
61D THR 3.1 12.1 - - - -
62D VAL* 3.8 5.4 - - - -
147D VAL* 5.6 0.2 - - - +
148D ALA* 4.3 6.4 - - - -
151D THR* 5.0 7.3 + - - +
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D SER* 1.3 75.6 - - - +
35D PRO* 1.3 70.6 - - + +
60D MET* 3.3 3.3 - - - -
61D THR 2.8 30.7 + - - -
144D SER* 3.3 26.9 - - - +
147D VAL* 3.7 11.7 - - + -
148D ALA* 3.6 13.4 - - - +
190D SER* 3.5 15.3 - - - +
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Residues in contact with PRO 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA* 1.3 85.4 - - - +
36D GLY* 1.3 68.2 + - - +
56D ALA* 3.6 23.8 - - + -
57D LEU 3.3 20.6 - - - +
59D LEU 3.3 6.3 - - - +
60D MET* 3.9 5.4 - - + -
140D SER* 4.8 0.5 - - - +
144D SER* 3.2 11.4 + - - -
189D ILE 4.8 0.2 - - - +
190D SER* 3.0 47.7 + - - +
193D GLY* 5.7 1.8 - - - -
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Residues in contact with GLY 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PRO* 1.3 80.1 - - - +
37D ARG* 1.3 60.6 + - - +
56D ALA* 3.5 3.1 - - - -
57D LEU* 2.8 28.7 + - - -
59D LEU* 2.6 18.8 + - - -
133D VAL* 3.9 13.7 - - - +
139D LEU 3.3 14.8 - - - -
140D SER* 4.4 5.4 - - - -
189D ILE* 5.5 0.3 - - - +
190D SER* 5.8 1.0 - - - -
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Residues in contact with ARG 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLY* 1.3 74.2 - - - +
38D VAL* 1.3 71.0 + - - +
39D ASN* 2.8 46.8 - - - +
43D GLU* 4.7 0.4 + - - -
54D PRO* 4.0 7.0 - - + -
55D MET 3.7 6.3 - - - +
56D ALA* 4.6 0.4 - - - +
57D LEU* 3.6 4.6 - - - +
138D GLY* 3.6 17.4 + - - -
139D LEU* 3.1 29.6 + - - +
140D SER* 3.6 22.2 - - - +
185D MET* 5.1 1.6 - - - -
186D ASP* 2.4 44.4 + - - +
189D ILE* 3.5 33.2 - - + -
190D SER* 5.7 1.1 - - - +
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 1.3 80.1 - - - +
39D ASN* 1.3 70.2 + - - +
40D LEU* 3.7 14.2 + - + -
54D PRO* 3.4 0.9 - - - +
55D MET* 2.8 51.1 + - + +
57D LEU* 3.6 25.5 - - + +
139D LEU* 4.5 8.7 - - + -
220D VAL* 4.6 6.1 - - + -
222D ILE* 4.0 22.0 - - + -
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Residues in contact with ASN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 2.8 40.6 - - - +
38D VAL* 1.3 81.3 - - - +
40D LEU* 1.3 65.1 + - - +
41D ILE 4.6 2.2 - - - +
43D GLU* 2.8 58.2 + - + +
52D VAL* 4.7 4.7 - - - +
53D LEU 4.7 0.6 - - - +
54D PRO* 3.2 27.2 - - + +
185D MET* 5.6 4.4 - - - +
186D ASP* 4.5 2.5 + - - +
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 4.4 18.8 - - + -
39D ASN* 1.3 74.5 - - - +
41D ILE* 1.3 64.7 + - + +
53D LEU* 2.9 33.2 + - + +
55D MET* 4.5 24.0 - - + -
198D ALA* 4.2 23.1 - - + -
213D LEU* 5.3 5.6 - - + -
220D VAL* 4.7 14.8 - - + -
295D LEU* 5.1 5.8 - - + -
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Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASN* 3.4 2.5 - - - +
40D LEU* 1.3 81.1 + - + +
42D GLY* 1.3 65.1 + - - +
43D GLU* 3.4 8.7 + - - -
52D VAL* 3.8 0.2 - - - -
53D LEU* 3.0 44.0 + - + -
284D GLU* 3.3 15.7 - - - +
287D ARG* 3.9 39.5 - - + +
288D THR* 3.8 15.2 + - + +
291D ALA* 4.1 20.0 - - + -
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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