Contacts of the helix formed by residues 111 - 122 (chain B) in PDB entry 1RQD
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 GLY 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.4 6.0 - - - +
32A ARG 4.0 2.0 - - - -
33A GLY* 3.3 39.4 - - - -
52A THR* 2.7 25.7 + - - -
110B SER* 1.3 66.7 - - - +
112B ILE* 1.3 51.7 + - - +
113B ARG 2.7 16.0 + - - -
114B GLU* 2.9 19.5 + - - +
115B THR* 3.8 2.0 + - - -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A THR* 3.9 5.8 - - + +
107B LEU* 3.3 27.4 - - + +
110B SER* 3.0 12.6 - - - +
111B GLY* 1.3 75.2 - - - +
113B ARG* 1.3 61.6 + - - +
114B GLU 3.2 0.4 - - - -
115B THR* 3.3 6.9 + - - +
116B ILE* 3.0 35.7 + - + +
281B LEU* 4.6 4.9 - - + -
343B ALA 3.7 15.9 - - - +
344B SER* 3.7 20.4 - - - +
347B PHE* 3.8 24.0 - - + -
348B PRO* 3.6 32.5 - - + -
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.8 12.9 - - - +
107B LEU 3.6 1.8 + - - -
108B ILE* 3.6 33.9 - - + +
110B SER 3.2 16.5 + - - +
111B GLY 2.7 0.4 + - - -
112B ILE* 1.3 78.5 - - - +
114B GLU* 1.3 80.5 + - - +
116B ILE 3.8 0.2 - - - -
117B ARG* 2.8 34.7 + - - +
138B ASP* 2.9 43.8 + - - +
141B LYS* 3.5 36.1 + - - +
142B CYS* 3.4 19.8 - - - -
218B GLU* 3.1 29.0 + - - +
220B VAL* 3.6 9.0 - - + +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 4.7 1.9 - - - +
32A ARG* 3.2 37.5 + - - +
33A GLY 3.1 38.6 + - - +
34A TYR 3.7 12.1 - - - +
35A ASP* 4.8 5.0 - - + +
110B SER 4.8 0.2 - - - +
111B GLY* 2.9 13.0 + - - +
113B ARG* 1.3 114.3 + - - +
115B THR* 1.3 64.5 + - - +
117B ARG* 3.5 15.5 + - - +
118B TYR* 3.0 25.1 + - - +
141B LYS* 5.0 1.4 + - - +
218B GLU 4.4 3.1 - - - +
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY* 5.5 0.2 - - - -
34A TYR* 4.2 14.1 + - - +
36A PHE* 4.6 6.9 - - + -
111B GLY 4.3 2.1 + - - -
112B ILE* 3.3 17.7 + - - +
114B GLU* 1.3 79.6 - - - +
116B ILE* 1.3 60.3 + - - +
118B TYR* 3.5 12.1 - - - +
119B LEU* 3.4 16.5 - - - +
347B PHE* 3.3 34.5 - - + -
348B PRO* 4.1 23.2 - - + +
351B VAL* 3.6 23.3 - - + -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.0 13.7 - - + -
103B TYR* 3.5 61.9 - - + -
107B LEU* 5.0 2.7 - - + -
108B ILE* 4.3 7.4 - - + -
112B ILE* 3.0 38.3 + - + +
113B ARG 3.9 2.7 - - - +
115B THR* 1.3 74.0 - - - +
117B ARG* 1.3 69.3 + - - +
118B TYR 3.1 0.4 + - - -
119B LEU* 3.2 7.6 + - - +
120B VAL* 3.1 23.5 + - + +
220B VAL* 4.1 17.0 - - + -
281B LEU* 4.8 2.5 - - + -
347B PHE* 4.2 11.4 - - + -
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.3 29.3 - - - +
35A ASP* 3.8 17.4 + - - -
37A ASN* 2.8 32.7 - - - +
113B ARG 2.8 20.0 + - - +
114B GLU* 3.5 18.1 + - - +
116B ILE* 1.3 78.6 - - - +
118B TYR* 1.3 51.7 + - - +
120B VAL* 3.3 2.1 + - - +
121B GLN* 2.7 55.4 + - - +
217B PRO 3.5 19.8 + - - -
218B GLU* 3.7 27.0 + - - +
219B SER 3.9 3.8 - - - -
220B VAL* 3.6 27.6 - - + +
223B TRP* 3.7 6.8 - - + -
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASP* 5.1 1.6 - - - +
36A PHE* 3.3 44.2 + + + +
37A ASN* 3.6 13.2 - - - +
114B GLU 3.0 11.5 + - - +
115B THR* 3.5 11.4 - - - +
116B ILE 3.1 0.2 - - - -
117B ARG* 1.3 74.2 - - - +
119B LEU* 1.3 84.7 + - + +
121B GLN* 3.1 21.3 + - - +
122B HIS* 3.1 35.7 + + - -
124B MET* 3.8 20.7 - - + +
351B VAL* 4.4 11.0 - - + -
356B ALA* 3.4 23.8 + - - +
359B MET* 2.9 43.8 - - + +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 4.0 18.4 - - + -
115B THR 3.4 12.6 - - - +
116B ILE* 3.2 5.3 + - - +
118B TYR* 1.3 95.9 - - + +
120B VAL* 1.3 60.7 + - - +
122B HIS 3.6 0.2 + - - -
123B ASN 3.4 2.4 + - - -
124B MET* 2.9 40.0 + - + +
125B VAL* 4.0 20.2 + - + -
279B ILE* 6.0 0.9 - - + -
347B PHE* 3.8 29.2 - - + -
351B VAL* 4.0 12.3 - - + -
355B PHE* 3.8 36.6 - - + -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 3.1 17.1 + - + +
117B ARG 3.6 6.5 - - - +
119B LEU* 1.3 74.7 - - + +
121B GLN* 1.3 55.8 + - - +
123B ASN 3.1 6.8 + - - -
125B VAL* 4.3 5.8 - - + -
128B LEU* 3.5 34.3 - - + -
220B VAL* 3.7 16.8 - - + +
223B TRP* 3.9 0.9 - - + -
224B ALA* 3.4 41.5 - - + +
227B ASN* 2.7 28.4 + - - -
229B ILE* 3.5 17.3 - - + +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 2.7 37.9 + - - +
117B ARG* 2.7 33.1 + - - +
118B TYR* 3.3 7.6 - - - +
120B VAL* 1.3 77.6 - - - +
122B HIS* 1.3 74.8 + - + +
223B TRP* 3.5 56.5 - - + +
227B ASN* 3.2 12.9 + - - +
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 2.6 28.0 + - - -
118B TYR* 3.1 47.6 + + - +
120B VAL 3.2 0.2 - - - -
121B GLN* 1.3 97.0 + - + +
123B ASN* 1.3 71.0 + - - +
124B MET* 3.1 24.0 + - + +
359B MET* 4.0 17.1 - - + +
362B PHE* 4.0 22.5 - - + +
363B MET* 4.8 21.5 - - + +
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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