Contacts of the strand formed by residues 136 - 143 (chain h) in PDB entry 5GJQ
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 CYS 136 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32h ILE* 4.0 4.4 - - - +
80h MET* 4.1 5.2 - - + -
81h THR 3.3 8.1 - - - +
83h MET 4.2 0.9 - - - +
86h ASP* 3.9 17.0 - - + -
87h SER* 3.3 27.8 - - - +
90h GLN* 3.5 36.5 + - - +
134h LEU* 3.0 20.6 + - - +
135h GLY* 1.3 78.7 - - - +
137h CYS* 1.3 61.1 + - - +
155h ASP 4.5 1.0 - - - -
156h PRO* 3.1 26.2 - - - +
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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
----------------------------------------------------------
32h ILE* 3.7 18.2 - - + -
79h VAL 3.5 1.6 - - - +
80h MET* 3.4 7.8 - - - -
81h THR* 2.8 40.7 + - - +
90h GLN* 5.0 0.4 - - - -
136h CYS* 1.3 77.4 - - - +
138h MET* 1.3 63.2 + - - +
139h ILE* 4.9 1.6 - - - +
153h LYS* 3.6 35.4 - - - -
154h CYS 3.7 15.3 - - - +
155h ASP* 4.5 3.8 - - - -
156h PRO* 5.1 0.4 - - + -
168h ALA* 4.1 14.8 - - + -
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Residues in contact with MET 138 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72h ILE* 4.8 0.9 - - + -
78h CYS* 4.3 8.5 - - + -
79h VAL 3.6 3.1 - - - -
80h MET* 3.5 28.0 - - + -
90h GLN* 3.6 39.4 + - + +
91h VAL* 4.3 4.3 - - - -
94h ALA* 3.9 12.1 - - + -
115h CYS* 5.1 0.3 - - - -
118h ILE* 4.2 19.7 - - - -
137h CYS* 1.3 73.4 - - - +
139h ILE* 1.3 62.7 + - - +
140h LEU* 3.7 39.4 + - + -
153h LYS* 3.2 5.4 - - - +
154h CYS* 2.9 47.9 + - - -
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Residues in contact with ILE 139 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39h SER* 5.1 3.6 - - - +
41h ALA* 3.9 20.0 - - + -
50h ILE* 3.9 23.5 - - + +
78h CYS* 3.2 3.1 - - - -
79h VAL* 2.9 48.0 + - + +
81h THR* 6.0 0.4 - - - +
137h CYS* 4.9 3.6 - - - +
138h MET* 1.3 73.8 - - - +
140h LEU* 1.3 66.2 + - - +
141h ILE 4.2 0.2 + - - -
151h VAL* 4.0 9.6 - - + -
152h TYR 3.2 9.6 - - - +
153h LYS* 3.6 35.4 - - + -
166h THR* 4.6 5.4 - - - -
167h ALA* 4.5 9.9 - - - -
168h ALA* 4.3 16.8 - - + +
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Residues in contact with LEU 140 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72h ILE* 4.1 4.5 - - + -
76h ILE* 4.0 16.2 - - + -
77h GLY 3.4 5.2 - - - +
78h CYS* 3.4 25.1 - - + -
111h VAL* 3.7 20.0 - - + +
114h LEU* 4.0 16.4 - - + -
115h CYS* 3.8 42.6 - - + +
138h MET* 3.7 26.2 - - + -
139h ILE* 1.3 74.9 - - - +
141h ILE* 1.3 61.2 + - - +
150h GLN 3.7 0.3 - - - +
151h VAL* 3.3 5.4 - - - +
152h TYR* 2.8 34.1 + - + +
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Residues in contact with ILE 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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48h ALA* 3.9 19.3 - - + +
49h VAL 4.9 1.6 - - - +
50h ILE* 3.4 43.5 - - + -
75h ASN 4.3 0.2 - - - +
76h ILE* 3.6 3.6 - - - +
77h GLY* 2.8 40.1 + - - +
111h VAL* 4.5 4.5 - - - -
140h LEU* 1.3 79.9 - - - +
142h GLY* 1.3 59.7 + - - +
150h GLN 3.2 5.4 - - - +
151h VAL* 3.8 23.1 - - + -
219h VAL* 4.2 4.7 - - - -
220h VAL* 3.7 20.5 - - + +
227h PHE* 3.8 20.0 - - + -
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Residues in contact with GLY 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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75h ASN 3.8 13.2 - - - -
111h VAL* 4.0 16.7 - - - +
141h ILE* 1.3 77.4 - - - +
143h ILE* 1.3 66.0 - - - -
144h ASP 3.9 0.2 - - - -
149h PRO* 3.7 0.3 - - - +
150h GLN* 2.8 37.1 + - - +
220h VAL* 3.9 10.8 - - - +
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Residues in contact with ILE 143 (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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47h CYS* 4.7 0.9 - - - -
75h ASN* 4.2 9.8 + - - +
111h VAL* 5.6 2.0 - - - -
142h GLY* 1.3 74.9 - - - -
144h ASP* 1.3 73.7 + - - +
145h GLU 4.1 0.2 + - - -
148h GLY* 3.7 9.0 - - - +
149h PRO* 3.8 26.7 - - + -
220h VAL* 3.6 26.8 - - + +
221h THR 3.2 33.0 - - - +
222h VAL* 4.1 21.8 - - + +
225h PRO* 4.2 17.4 - - + +
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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