Contacts of the strand formed by residues 117 - 129 (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 VAL 117 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112H LYS 3.9 0.7 - - - +
113H THR* 3.3 3.9 - - - -
114H LYS 3.0 31.5 + - - +
115H ASP* 3.7 11.7 - - + +
116H GLY* 1.3 83.8 - - - +
118H VAL* 1.3 75.3 + - - +
119H GLU* 3.9 3.0 + - + +
141H LYS* 3.9 26.2 - - + -
142H TYR 3.3 13.9 - - - +
143H THR* 4.2 18.6 - - + +
144H LEU* 4.4 0.4 - - - +
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Residues in contact with VAL 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H TRP* 4.3 9.0 - - + -
97H VAL* 6.1 0.2 - - + -
111H VAL* 3.9 27.1 - - + -
112H LYS 3.6 4.5 - - - +
113H THR* 3.9 10.8 - - - +
117H VAL* 1.3 72.4 - - - +
119H GLU* 1.3 61.7 + - - +
120H ILE* 4.2 14.8 + - + -
140H ARG 3.7 0.7 - - - +
141H LYS* 3.2 6.6 - - - -
142H TYR* 2.8 46.5 + - + +
144H LEU* 3.6 37.9 - - + -
153H VAL* 4.9 6.7 - - + -
165H VAL* 4.3 11.2 - - + -
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Residues in contact with GLU 119 (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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110H THR* 3.6 1.7 - - - +
111H VAL* 3.4 4.5 - - - +
112H LYS* 2.7 52.8 + - + +
117H VAL* 3.9 3.3 + - + +
118H VAL* 1.3 73.2 - - - +
120H ILE* 1.3 63.2 + - - +
121H THR* 4.2 13.3 - - + +
139H THR* 4.0 22.7 - - + +
140H ARG 3.4 2.5 - - - -
141H LYS* 3.4 30.9 + - + -
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Residues in contact with ILE 120 (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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97H VAL* 5.2 2.2 - - + -
99H LEU* 4.4 12.6 - - + -
109H LEU* 5.1 2.7 - - + -
110H THR 3.3 8.5 - - - +
111H VAL* 4.2 8.1 - - + -
118H VAL* 4.2 13.0 - - + -
119H GLU* 1.3 76.6 - - - +
121H THR* 1.3 67.5 + - - +
138H PHE* 3.7 20.6 - - + -
139H THR* 3.3 3.1 - - - -
140H ARG* 2.7 47.6 + - + +
142H TYR* 3.8 29.4 - - + -
163H LEU* 3.8 25.1 - - + -
165H VAL* 4.3 21.3 - - + -
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Residues in contact with THR 121 (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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108H GLU 3.8 0.7 - - - +
109H LEU* 3.4 4.6 - - - +
110H THR* 2.9 47.8 + - + +
119H GLU* 4.2 18.2 - - + +
120H ILE* 1.3 80.3 - - - +
122H GLY* 1.3 60.3 + - - +
138H PHE* 3.4 10.3 - - - -
139H THR* 3.7 23.1 - - + +
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Residues in contact with GLY 122 (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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104H PHE* 3.6 9.6 - - - -
108H GLU 3.3 9.9 - - - -
109H LEU* 4.0 4.3 - - - -
121H THR* 1.3 76.0 - - - +
123H LYS* 1.3 62.2 + - - +
137H CYS* 3.3 3.6 - - - +
138H PHE* 3.0 50.8 + - - +
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Residues in contact with LYS 123 (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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104H PHE* 3.5 5.7 - - - -
108H GLU* 3.2 29.0 + - - +
122H GLY* 1.3 76.3 - - - +
124H HIS* 1.3 66.9 + - - +
136H ARG 3.4 12.3 - - - +
137H CYS* 4.4 11.4 - - + -
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Residues in contact with HIS 124 (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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103H HIS* 3.5 19.1 + - + -
104H PHE* 3.7 23.6 - + + -
108H GLU* 3.4 30.1 - - - +
123H LYS* 1.3 79.4 - - - +
125H GLU* 1.3 79.4 + - - +
127H ARG* 3.5 20.1 + - + +
134H ILE* 3.4 24.7 - - + -
135H SER* 3.4 24.5 - - - -
136H ARG* 3.2 45.4 + - + +
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Residues in contact with GLU 125 (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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108H GLU* 4.7 1.5 + - - +
124H HIS* 1.3 99.1 + - - +
126H GLU* 1.3 77.6 + - - +
127H ARG* 3.3 14.4 + - - +
135H SER* 3.8 4.7 - - - -
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Residues in contact with GLU 126 (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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151F THR* 5.1 7.4 - - - +
139G THR* 5.3 4.0 - - - +
141G LYS* 2.7 48.5 + - + +
125H GLU* 1.3 84.7 - - - +
127H ARG* 1.3 61.1 + - - +
133H TYR* 4.2 33.8 - - + +
134H ILE* 3.6 13.7 - - - +
135H SER* 3.9 10.1 - - - +
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Residues in contact with ARG 127 (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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103H HIS 3.2 24.7 + - - -
105H ALA* 5.2 2.4 - - - +
108H GLU* 2.6 38.9 + - - -
124H HIS* 3.5 21.4 - - + +
125H GLU* 3.6 18.0 + - + +
126H GLU* 1.3 77.3 - - - +
128H GLN* 1.3 74.4 + - - +
133H TYR* 4.1 6.6 - - - -
134H ILE* 3.0 37.6 + - - +
76L ALA 4.9 10.5 - - - +
77L LEU* 3.7 26.3 - - - +
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Residues in contact with GLN 128 (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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111F VAL 4.3 4.2 - - - +
112F LYS* 3.8 30.3 + - + +
113F THR* 3.0 46.0 + - - +
114F LYS* 5.4 3.2 - - - +
150F PRO 5.0 0.7 - - - +
127H ARG* 1.3 83.8 - - - +
129H ASP* 1.3 63.9 + - - +
132H GLY* 3.4 8.6 - - - +
133H TYR* 3.4 51.3 + - + +
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Residues in contact with ASP 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F THR* 4.8 0.3 - - - +
111F VAL 5.5 0.9 - - - +
112F LYS* 3.6 22.1 - - - +
140G ARG* 2.8 30.3 + - - -
103H HIS* 4.7 10.3 + - + -
127H ARG 3.6 0.8 + - - +
128H GLN* 1.3 77.7 - - - +
130H GLU* 1.3 77.4 + - - +
131H HIS* 2.9 18.5 + - - -
132H GLY* 2.9 25.9 + - - +
134H ILE* 3.9 6.5 - - + -
136H ARG* 3.1 19.7 + - - +
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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
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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