Contacts of the strand formed by residues 95 - 101 (chain P) in PDB entry 1SVC
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 LYS 95 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94P ALA* 1.3 72.9 - - - +
96P VAL* 1.3 58.5 + - - +
97P ILE* 4.2 4.7 - - + -
125P THR* 3.7 27.4 - - + -
126P VAL 3.9 4.5 - - - +
127P THR* 4.6 9.6 - - + +
166P TYR* 2.7 34.1 + - - -
218P THR 3.4 3.3 - - - +
219P ALA* 4.4 0.2 - - - -
220P PHE* 2.7 57.9 + - + +
228P PHE* 4.2 26.9 + - + +
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Residues in contact with VAL 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P LEU* 3.7 30.3 - - + -
85P VAL* 4.7 10.1 - - + -
87P ILE* 4.4 13.5 - - + -
94P ALA 3.9 0.8 - - - +
95P LYS* 1.3 70.6 - - - +
97P ILE* 1.3 62.9 + - - +
124P CYS 4.0 0.3 - - - +
125P THR* 3.8 1.7 - - - +
126P VAL* 2.9 61.0 + - + +
127P THR 4.8 2.7 - - - -
128P ALA* 4.8 2.0 - - + +
135P VAL* 4.1 22.2 - - + -
137P PHE* 4.6 11.7 - - + -
217P PHE* 5.3 2.9 - - + -
218P THR 3.2 2.2 - - - +
219P ALA* 4.0 8.7 - - + -
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Residues in contact with ILE 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P LYS* 4.2 9.0 - - + -
96P VAL* 1.3 75.4 - - - +
98P VAL* 1.3 63.6 + - - +
99P GLN* 3.7 23.8 - - + +
123P ILE* 4.4 3.6 - - + -
124P CYS 3.2 7.2 - - - +
125P THR* 3.6 28.7 - - + +
166P TYR* 3.5 50.7 - - + +
167P ASN* 4.7 0.2 - - - +
216P MET 3.3 0.3 - - - +
217P PHE* 3.0 28.4 - - - +
218P THR* 2.9 30.0 + - - +
220P PHE* 3.7 15.5 - - + -
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Residues in contact with VAL 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97P ILE* 1.3 78.2 - - - +
99P GLN* 1.3 63.2 + - - +
114P LEU* 3.6 25.3 - - + +
123P ILE* 3.0 22.0 - - - +
124P CYS* 2.9 26.3 + - + +
137P PHE* 3.4 27.6 - - + -
140P LEU* 4.7 3.6 - - + -
215P LEU* 3.7 23.6 - - + -
216P MET 3.3 2.9 - - - +
217P PHE* 3.4 36.1 - - + -
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Residues in contact with GLN 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97P ILE* 3.7 15.1 - - + +
98P VAL* 1.3 78.4 - - - +
100P LEU* 1.3 65.2 + - - +
101P VAL* 3.5 3.4 + - + -
109P LEU* 3.8 16.2 - - + +
114P LEU* 4.7 2.9 - - - -
122P GLY 5.0 2.7 - - - -
123P ILE* 3.9 21.2 - - + +
161P ALA* 4.0 7.3 - - - +
166P TYR* 3.4 23.3 + - - +
167P ASN* 3.6 22.2 + - - -
171P LEU* 3.2 25.0 - - - +
214P ARG 3.5 1.6 - - - +
215P LEU* 3.7 2.4 - - - -
216P MET* 3.0 42.5 + - + +
218P THR* 4.2 5.3 + - - -
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Residues in contact with LEU 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P GLN* 1.3 71.6 - - - +
101P VAL* 1.3 60.2 + - - +
109P LEU* 3.7 11.1 - - - +
110P HIS* 2.8 29.4 + - + +
112P HIS* 3.5 31.0 - - + +
113P SER 3.4 35.2 - - - +
114P LEU* 3.6 23.7 - - + +
122P GLY 4.9 4.5 + - - +
142P ILE* 4.0 11.2 - - + -
213P VAL* 3.6 30.7 - - + -
214P ARG 3.6 6.1 - - - +
215P LEU* 4.2 12.1 - - + -
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Residues in contact with VAL 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P GLN* 4.1 6.3 - - + +
100P LEU* 1.3 78.9 - - - +
102P THR* 1.3 65.6 + - - +
107P ILE* 3.9 10.8 - - + -
108P HIS 3.5 10.3 - - - +
109P LEU* 4.9 0.4 - - - -
110P HIS* 3.8 7.5 + - - +
171P LEU* 3.8 26.7 - - + -
213P VAL* 3.7 5.7 - - - -
214P ARG* 3.0 55.2 + - + +
216P MET* 3.7 25.8 - - + -
236P VAL* 3.9 15.0 - - + -
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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