Contacts of the strand formed by residues 92 - 100 (chain H) in PDB entry 1G9N
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 ALA 92 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 4.3 9.4 - - - +
39H GLN 3.1 31.0 - - - +
40H ALA* 3.4 7.2 - - + +
41H PRO* 4.3 4.5 - - - -
90H ASP 3.0 9.9 + - - +
91H THR* 1.3 78.6 - - - +
93H VAL* 1.3 61.2 + - - +
94H TYR* 3.4 13.8 - - + -
123H LEU* 3.5 8.7 - - - -
124H VAL 2.9 29.9 + - - -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 2.9 36.6 + - + +
41H PRO* 6.2 0.9 - - + -
92H ALA* 1.3 72.3 - - - +
94H TYR* 1.3 61.7 + - - +
95H PHE* 3.4 43.8 + - + -
120H GLN 5.5 0.2 - - - +
121H GLY* 4.3 2.7 - - - -
122H THR 3.5 16.4 - - - +
123H LEU* 4.0 23.6 - - + +
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Residues in contact with TYR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLU* 2.8 21.1 - - - +
18H VAL* 5.8 2.9 - - + -
20H VAL* 4.8 8.3 - - + -
36H TRP* 3.6 14.8 - + + -
37H VAL 3.9 2.5 - - - -
38H ARG* 2.8 35.4 + - + -
48H MET* 3.2 42.2 - - + -
81H LEU* 4.1 12.8 - - + -
83H LEU* 3.4 15.3 - - + +
86H LEU* 5.4 1.3 - - + +
90H ASP* 2.5 32.1 + - - +
92H ALA 3.4 17.9 - - - -
93H VAL* 1.3 68.7 - - - +
95H PHE* 1.3 62.1 - - - +
122H THR* 2.6 23.8 + - - +
124H VAL* 3.8 28.3 - - + -
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Residues in contact with PHE 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 3.9 1.3 - - - -
36H TRP* 3.0 10.2 - - - -
37H VAL* 2.7 45.6 + - + +
39H GLN* 3.7 17.9 - - + -
45H LEU* 4.7 0.9 - - + -
93H VAL* 3.4 33.4 + - + -
94H TYR* 1.3 73.0 - - - +
96H CYS* 1.3 59.8 + - - +
118H TRP* 3.7 24.7 - + + -
119H GLY 3.9 10.5 - - - -
120H GLN 4.0 5.2 - - - -
121H GLY* 3.4 19.3 - - - -
38L GLN* 3.6 28.5 - - - -
41L GLY 6.1 0.7 - - - -
42L GLN 3.9 7.6 - - - -
43L ALA* 3.6 20.6 - - + -
44L PRO* 4.2 7.2 - - + -
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Residues in contact with CYS 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.7 6.1 - - - +
6H GLU* 3.3 16.9 + - + +
22H CYS* 2.0 50.9 - - - -
34H PHE* 4.7 11.0 - - - -
35H THR 3.9 2.5 - - - -
36H TRP* 3.6 26.7 - - + -
79H VAL* 5.0 2.2 - - - -
95H PHE* 1.3 72.8 - - - +
97H ALA* 1.3 64.6 + - - +
118H TRP* 3.3 2.1 - - - +
119H GLY* 2.5 34.0 + - - -
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Residues in contact with ALA 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.0 3.1 - - - -
34H PHE* 3.2 5.8 - - - +
35H THR* 2.5 45.9 + - - +
37H VAL* 5.1 0.7 - - + -
95H PHE 5.3 0.2 - - - +
96H CYS* 1.3 77.4 - - - +
98H GLY* 1.3 56.7 + - - +
115H LEU* 3.3 35.9 - - + -
117H HIS 3.1 5.6 - - - +
118H TRP* 3.6 23.3 - - + -
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Residues in contact with GLY 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.9 3.0 - - - +
32H TYR* 4.7 3.1 - - - -
33H SER 3.4 10.3 - - - -
34H PHE* 4.1 14.8 - - - -
97H ALA* 1.3 76.6 - - - +
99H VAL* 1.3 60.6 + - - -
115H LEU* 4.5 4.3 - - - -
116H LYS 3.0 6.7 + - - -
117H HIS* 2.5 46.3 + - - +
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Residues in contact with VAL 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H TYR* 3.1 17.6 - - - -
33H SER* 3.1 40.9 + - - +
50H ARG* 5.1 0.2 - - - +
98H GLY* 1.3 75.3 - - - +
100H TYR* 1.3 75.1 + - + +
101H GLU* 4.0 0.7 - - - +
112H ASN* 4.0 15.3 - - + +
114H PHE* 3.5 53.4 - - + +
115H LEU* 5.4 1.6 - - + -
116H LYS* 4.0 13.0 - - + +
117H HIS* 4.9 0.2 - - - -
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Residues in contact with TYR 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ASP* 4.0 9.9 - - - -
31H ARG* 3.3 55.2 + - + -
32H TYR* 3.4 33.3 - + + +
99H VAL* 1.3 80.0 - - + +
101H GLU* 1.3 59.7 + - - +
102H GLY* 3.6 31.0 - - - -
103H GLU* 4.1 7.6 + - - -
110H ARG* 5.0 11.0 - - - -
112H ASN* 3.2 20.4 + - - -
116H LYS* 5.2 1.8 - - - +
117H HIS* 5.3 1.7 - - - +
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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
------------------------------------------------------------
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