Contacts of the strand formed by residues 30 - 41 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391B CYS* 4.0 28.3 - - + -
28C PRO 3.5 1.0 - - - -
29C GLU* 1.3 86.4 - - + +
31C ALA* 1.3 64.9 + - - +
32C VAL* 3.9 17.7 - - + -
64C VAL* 3.4 5.0 - - - +
65C GLY 3.0 37.0 + - - +
67C PRO* 5.3 4.3 - - + -
152C PHE* 3.6 33.7 - - + -
155C GLN* 4.1 29.6 - - + +
156C LEU* 4.9 10.1 - - + -
390C LEU 3.9 4.9 - - - +
392C LEU* 3.7 8.0 - - - +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.9 17.0 - - + -
30C LEU* 1.3 74.2 - - - +
32C VAL* 1.3 70.9 + - - +
62C VAL* 5.0 0.7 - - + -
63C LEU 3.4 5.4 - - - +
64C VAL* 3.6 19.5 - - + -
389C VAL* 4.0 1.9 - - - +
390C LEU* 2.8 46.1 + - + +
392C LEU* 3.9 10.8 - - + -
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.9 17.9 - - + -
31C ALA* 1.3 80.0 - - - +
33C SER* 1.3 62.3 + - - +
62C VAL* 3.3 10.5 - - - +
63C LEU* 2.8 49.1 + - + +
148C ALA* 3.3 30.3 - - - +
151C THR* 3.9 28.9 - - + +
152C PHE* 4.0 7.0 - - + +
155C GLN* 4.6 0.4 - - + -
388C LYS 3.3 11.7 - - - +
389C VAL* 4.1 9.6 - - + -
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Residues in contact with SER 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 1.3 78.9 - - - +
34C ALA* 1.3 62.3 + - - +
35C PRO* 4.8 0.2 - - - -
60C MET* 3.6 33.0 - - - +
61C THR 3.2 9.9 - - - -
62C VAL* 3.9 5.8 - - - -
148C ALA* 4.4 3.6 - - - -
151C THR* 4.8 1.7 + - - -
386C GLY 4.9 1.7 + - - -
387C ALA* 3.3 4.7 - - - +
388C LYS* 3.0 50.4 + - - +
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER* 1.3 76.9 - - - +
35C PRO* 1.3 63.8 - - + +
60C MET* 4.0 2.9 - - - -
61C THR* 2.8 32.3 + - - +
144C SER* 3.3 12.8 - - - +
147C VAL* 3.7 10.8 - - + -
148C ALA* 3.4 28.4 - - - +
190C SER* 3.3 19.1 - - - +
387C ALA* 4.4 1.3 - - + +
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Residues in contact with PRO 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ALA* 1.3 85.8 - - - +
36C GLY* 1.3 65.0 - - - +
56C ALA* 3.7 13.5 - - + -
57C LEU 3.2 26.5 - - - +
59C LEU 3.3 7.2 - - - +
60C MET* 3.8 6.5 - - + -
140C SER* 4.7 0.5 - - - +
144C SER* 3.2 8.9 + - - -
190C SER* 3.0 48.8 + - - +
385C ASP 3.3 20.0 - - - +
386C GLY* 3.7 12.1 - - - +
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Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PRO* 1.3 80.0 - - - +
37C ARG* 1.3 62.2 + - - +
56C ALA* 3.8 2.3 - - - -
57C LEU* 3.1 27.0 + - - -
59C LEU* 2.8 15.2 + - - -
133C VAL* 3.8 14.5 - - - +
139C LEU 3.1 13.7 - - - -
140C SER* 3.9 10.5 - - - -
189C ILE* 5.7 0.2 - - - +
190C SER* 5.7 0.6 - - - -
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLY* 1.3 74.3 - - - +
38C VAL* 1.3 69.1 + - - +
39C ASN* 4.7 4.8 - - - +
54C PRO* 4.5 2.2 - - - -
55C MET 3.6 9.9 - - - +
57C LEU* 3.7 7.3 - - - +
138C GLY 3.6 13.0 + - - +
139C LEU* 2.8 38.4 + - - +
140C SER* 2.3 46.6 + - - +
185C MET* 3.4 24.5 - - - +
186C ASP* 2.6 31.1 + - - +
189C ILE* 3.6 34.1 - - + -
190C SER* 5.7 0.7 - - - +
345C GLY* 3.4 29.5 - - - +
346C GLY 4.6 1.4 - - - +
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG* 1.3 77.6 - - - +
39C ASN* 1.3 63.6 + - - +
40C LEU* 4.3 10.1 - - + -
54C PRO* 3.2 3.1 - - - +
55C MET* 2.9 60.8 + - + +
57C LEU* 3.9 9.9 - - + +
139C LEU* 4.5 2.5 - - + -
220C VAL* 4.6 2.2 - - + -
222C ILE* 3.6 24.7 - - + -
344C THR* 3.8 13.5 - - + +
353C VAL* 3.6 33.9 - - + -
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG* 4.4 4.9 - - - +
38C VAL* 1.3 74.4 - - - +
40C LEU* 1.3 59.3 + - - +
41C ILE 3.1 17.9 + - - +
42C GLY 3.0 31.9 + - - -
43C GLU* 3.0 25.6 + - - +
52C VAL* 4.4 0.4 - - - +
53C LEU 3.1 20.3 + - - -
54C PRO* 3.2 3.8 - - + -
185C MET* 3.4 26.5 - - + +
342C ARG* 2.8 16.6 + - - -
344C THR* 2.8 32.3 + - - +
345C GLY 4.5 1.6 - - - +
353C VAL* 3.7 2.6 - - - +
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 3.8 12.8 + - + -
39C ASN* 1.3 72.0 - - - +
41C ILE* 1.3 65.2 + - + +
53C LEU* 3.0 31.7 + - + +
55C MET* 4.6 10.8 - - + +
198C ALA* 3.9 25.1 - - + -
213C LEU* 4.2 13.9 - - + -
220C VAL* 4.3 30.3 - - + -
295C LEU* 4.9 6.5 - - + -
307C MET* 3.3 16.5 - - + +
342C ARG* 3.2 20.8 + - - -
353C VAL* 4.3 9.4 - - + -
355C LEU* 6.5 0.9 - - + -
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ASN* 3.1 7.0 - - - +
40C LEU* 1.3 84.1 - - + +
42C GLY* 1.3 61.5 + - - +
52C VAL 3.8 0.2 - - - -
53C LEU* 2.9 33.3 + - + +
284C GLU* 5.0 1.3 - - - +
287C ARG* 6.0 0.7 - - + -
288C THR* 4.1 7.9 - - + +
291C ALA* 4.6 20.9 - - + -
306C LEU* 5.9 2.0 - - + +
307C MET* 4.8 14.8 - - + +
310C SER* 5.4 2.5 - - - +
342C ARG* 3.7 11.2 - - - +
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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