Contacts of the strand formed by residues 132 - 143 (chain H) in PDB entry 6GJH
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 132 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111F VAL 5.8 3.8 + - - -
140G ARG* 3.4 4.4 + - - +
141G LYS 5.0 4.5 - - - -
142G TYR* 5.4 0.4 - - - -
127H ARG 3.6 0.9 - - - +
128H GLN* 3.4 10.0 - - - -
129H ASP* 2.9 35.1 + - - +
131H HIS* 1.3 78.8 - - - +
133H TYR* 1.3 66.8 + - - -
134H ILE 3.6 0.3 + - - -
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Residues in contact with TYR 133 (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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113F THR 4.5 0.2 + - - -
150F PRO* 3.7 29.1 - - - +
151F THR* 3.9 39.0 - - + +
140G ARG* 3.4 6.1 - - - +
141G LYS* 3.1 40.3 + - + +
126H GLU* 4.2 29.6 - - + +
127H ARG* 3.6 18.2 - - - -
128H GLN* 3.4 44.7 + - + -
132H GLY* 1.3 74.2 - - - -
134H ILE* 1.3 61.5 + - - +
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Residues in contact with ILE 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G LEU* 6.2 0.2 - - + -
138G PHE* 4.0 20.9 - - + -
139G THR 3.3 13.7 - - - +
140G ARG* 3.3 43.7 - - + +
124H HIS* 3.4 8.0 - - - -
126H GLU* 4.1 3.9 - - - +
127H ARG 3.0 38.1 + - - +
129H ASP* 3.7 13.0 - - + +
132H GLY 3.8 1.6 - - - +
133H TYR* 1.3 77.8 - - - +
135H SER* 1.3 73.8 + - - +
136H ARG* 3.9 30.3 - - + +
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Residues in contact with SER 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G PHE* 3.2 7.5 - - - +
139G THR* 3.0 46.0 + - - -
124H HIS* 3.4 18.4 - - - -
125H GLU* 3.8 13.0 - - - -
126H GLU* 3.9 8.3 - - - +
134H ILE* 1.3 73.8 - - - +
136H ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 136 (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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137G CYS* 3.4 9.0 - - - +
138G PHE* 4.3 5.8 - - + +
140G ARG* 3.9 8.9 - - - +
103H HIS* 3.3 50.9 + - - +
104H PHE* 3.8 18.1 - - + -
123H LYS* 3.4 3.8 - - - +
124H HIS* 3.2 59.8 + - - +
129H ASP* 3.1 26.5 + - - +
134H ILE* 3.9 23.0 - - + +
135H SER* 1.3 82.5 - - - +
137H CYS* 1.3 63.8 + - - +
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Residues in contact with CYS 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ARG* 3.5 2.6 - - - +
137G CYS* 2.0 77.2 + - - +
104H PHE* 4.8 1.1 - - - -
122H GLY 3.3 12.1 - - - +
123H LYS* 4.4 14.4 - - + -
136H ARG* 1.3 76.8 - - - +
138H PHE* 1.3 68.3 + - - +
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Residues in contact with PHE 138 (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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134G ILE* 4.4 9.6 - - + -
135G SER* 3.2 14.1 - - - +
136G ARG* 4.6 6.3 - - + -
99H LEU* 4.3 6.3 - - + -
101H VAL* 3.8 24.7 - - + -
104H PHE* 3.6 34.5 - + - -
109H LEU* 4.2 8.7 - - + -
120H ILE* 3.7 28.5 - - + -
121H THR* 3.4 2.3 - - - -
122H GLY* 3.0 51.4 + - - +
137H CYS* 1.3 79.4 - - - +
139H THR* 1.3 74.8 + - - +
140H ARG* 4.0 12.1 - - + -
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Residues in contact with THR 139 (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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126G GLU* 5.4 2.3 - - - +
133G TYR 3.8 0.7 - - - +
134G ILE* 3.4 6.2 - - - +
135G SER* 3.0 42.8 + - - -
119H GLU* 4.0 22.9 - - + +
120H ILE 3.3 4.0 - - - -
121H THR* 3.7 23.5 - - + +
138H PHE* 1.3 78.7 + - - +
140H ARG* 1.3 63.1 + - - +
141H LYS* 4.3 12.5 - - + +
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Residues in contact with ARG 140 (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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129G ASP* 2.9 41.8 + - - -
131G HIS* 3.7 21.2 - - - +
132G GLY 3.7 3.4 - - - +
133G TYR 3.4 11.0 + - - -
134G ILE* 3.9 26.2 - - + +
136G ARG* 4.3 8.5 - - - +
84H GLY 5.4 4.2 + - - -
86H SER* 5.1 5.0 - - - -
99H LEU* 4.8 11.5 - - + +
118H VAL 3.7 0.9 - - - +
119H GLU* 3.4 3.5 - - - +
120H ILE* 2.7 46.2 + - + +
138H PHE* 4.0 15.0 - - + -
139H THR* 1.3 73.4 - - - +
141H LYS* 1.3 67.2 + - - +
142H TYR* 3.3 46.1 + - + +
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Residues in contact with LYS 141 (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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126G GLU* 3.0 32.3 + - - +
132G GLY* 3.5 8.3 - - - -
133G TYR* 3.1 43.5 + - + +
117H VAL* 3.9 18.8 - - + -
118H VAL 3.2 4.9 - - - +
119H GLU* 3.4 33.6 + - + -
139H THR* 4.3 9.6 - - + -
140H ARG* 1.3 81.5 - - - +
142H TYR* 1.3 65.0 + - - +
143H THR* 5.9 0.2 - - - +
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Residues in contact with TYR 142 (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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131G HIS* 4.0 33.7 - - + -
132G GLY* 5.2 0.4 - - - -
86H SER* 2.9 24.1 + - - -
88H ILE* 4.4 7.4 - - + -
95H TRP* 3.9 25.8 - + + -
97H VAL* 3.7 29.1 - - + +
99H LEU* 3.9 8.9 - - + +
117H VAL* 3.3 5.6 - - - -
118H VAL* 2.8 46.7 + - + +
120H ILE* 3.8 24.9 - - + -
140H ARG* 3.3 40.0 + - + +
141H LYS* 1.3 76.8 - - - +
143H THR* 1.3 62.3 + - - +
144H LEU 3.7 0.3 + - - -
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Residues in contact with THR 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G HIS 5.7 0.6 + - - -
133G TYR* 5.1 17.3 - - + -
95H TRP* 4.5 10.2 + - - -
116H GLY 3.7 5.8 - - - -
117H VAL* 4.2 17.3 - - + +
141H LYS* 5.9 0.4 - - + -
142H TYR* 1.3 74.6 - - - +
144H LEU* 1.3 66.2 + - - +
145H PRO* 4.1 1.6 - - - +
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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