Contacts of the strand formed by residues 191 - 199 (chain A) in PDB entry 1GO4
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 HIS 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.2 7.0 - - + -
16A SER* 2.6 31.8 + - - +
17A ALA* 3.9 17.4 - - - -
20A VAL* 3.8 18.6 - - + +
76A LEU* 2.8 46.0 + - + -
79A CYS* 4.5 1.6 - - - -
104A ILE* 4.8 3.6 - - + -
105A GLU 3.4 2.7 - - - +
106A CYS* 3.4 33.1 - - + +
186A PHE* 4.2 1.2 - - - +
187A THR* 3.4 5.1 - - - -
188A THR* 3.0 29.7 + - - +
190A ILE* 1.3 88.9 - - + +
192A LYS* 1.3 63.9 + - - +
193A VAL* 5.0 0.4 - - + -
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Residues in contact with LYS 192 (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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103A ASP 3.6 0.7 - - - +
104A ILE* 3.4 5.2 - - - +
105A GLU* 2.9 60.9 + - + +
185A SER* 4.1 18.4 - - - -
186A PHE 3.5 10.8 - - - +
187A THR* 3.7 17.3 - - + +
191A HIS* 1.3 73.4 - - - +
193A VAL* 1.3 66.1 + - - +
194A ASN* 3.8 26.5 + - - +
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Residues in contact with VAL 193 (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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20A VAL* 4.0 23.6 - - + -
23A PHE* 4.0 15.0 - - + -
24A PHE* 4.2 10.3 - - + -
102A PHE* 4.6 0.7 - - + -
103A ASP 3.5 3.6 - - - +
104A ILE* 4.4 14.1 - - + -
184A ARG 4.4 0.5 - - - +
185A SER* 3.2 5.0 - - - -
186A PHE* 2.7 75.8 + - + -
191A HIS 5.0 0.4 - - - -
192A LYS* 1.3 81.1 - - - +
194A ASN* 1.3 74.9 + - - +
195A SER* 4.3 3.9 + - - +
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Residues in contact with ASN 194 (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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101A GLN 4.6 0.4 - - - -
102A PHE* 3.1 9.7 - - - +
103A ASP* 2.8 56.2 + - + +
105A GLU* 4.0 14.8 + - - +
182A ARG* 5.0 9.5 + - - -
183A LEU 5.7 0.6 - - - +
184A ARG 5.5 0.2 - - - -
185A SER* 3.4 19.9 - - - -
192A LYS* 3.8 27.0 + - - +
193A VAL* 1.3 77.6 - - - +
195A SER* 1.3 62.3 + - - +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.0 3.5 - - - -
100A TRP* 6.3 0.2 - - - -
101A GLN 3.9 3.6 - - - -
102A PHE* 3.2 30.0 - - - -
131A VAL* 3.7 18.7 - - - +
182A ARG* 3.8 1.6 - - - +
183A LEU* 2.8 52.9 + - - +
184A ARG 4.1 7.0 + - - -
193A VAL* 4.3 4.0 + - - +
194A ASN* 1.3 74.4 - - - +
196A MET* 1.3 64.7 + - - +
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Residues in contact with MET 196 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ARG 4.4 1.6 - - - +
100A TRP* 3.4 8.1 - - - +
101A GLN* 3.0 61.5 + - + +
102A PHE* 5.1 1.5 - - - -
103A ASP* 5.9 2.9 - - - +
180A GLU* 2.9 49.4 - - + +
181A VAL 3.3 14.1 - - - +
182A ARG* 3.9 15.9 - - + -
183A LEU* 4.4 2.2 - - - +
195A SER* 1.3 76.0 - - - +
197A VAL* 1.3 77.3 + - - +
198A ALA* 3.9 7.6 - - + +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLU* 4.1 8.7 - - + -
99A ARG 3.9 2.2 - - - -
100A TRP* 3.1 69.3 - - + +
138A THR* 4.9 8.7 - - + -
141A PHE* 6.0 1.3 - - + -
142A LEU* 4.4 12.3 - - + -
179A GLU 3.6 1.0 - - - +
180A GLU* 3.4 1.6 - - - -
181A VAL* 2.9 39.4 + - + +
183A LEU* 5.1 6.1 - - + -
196A MET* 1.3 78.9 - - - +
198A ALA* 1.3 71.5 + - - +
199A TYR* 3.9 6.8 - - + -
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Residues in contact with ALA 198 (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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98A GLU* 3.5 5.2 - - - +
99A ARG* 2.9 41.5 + - + +
175A ILE* 3.8 28.1 - - + +
178A SER* 4.0 5.2 - - - +
179A GLU 3.0 9.6 - - - +
180A GLU* 4.2 12.6 - - + +
196A MET* 3.9 6.9 - - + -
197A VAL* 1.3 72.9 - - - +
199A TYR* 1.3 60.3 + - - +
532G GLN* 6.2 0.4 - - + -
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Residues in contact with TYR 199 (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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97A LEU 4.0 6.5 - - - -
98A GLU* 3.6 22.9 - - + +
141A PHE* 3.8 34.0 - + - -
142A LEU* 3.4 22.2 - - + -
143A PRO* 3.8 21.8 - - + -
175A ILE* 4.3 0.4 - - - -
178A SER* 3.2 4.3 - - - -
179A GLU* 2.7 71.0 + - + +
181A VAL* 4.0 18.7 - - + +
197A VAL* 3.9 8.5 - - + -
198A ALA* 1.3 76.4 - - - +
200A LYS* 1.3 68.4 + - - +
201A ILE* 4.9 9.4 - - + -
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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