Contacts of the strand formed by residues 67 - 75 (chain G) in PDB entry 3HEI
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 ILE 67 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4G LEU* 3.7 29.4 - - + -
64G ALA* 3.9 11.7 - - + -
65G GLU 4.2 0.2 - - - -
66G ARG* 1.3 75.9 - - - +
68G PHE* 1.3 62.1 + - - +
69G ILE* 4.0 22.2 - - + +
96G TYR* 5.6 3.1 - - + -
142G SER* 3.1 7.3 - - - -
143G VAL* 2.9 50.9 + - + +
146G LEU* 3.7 26.9 - - + -
151G PHE* 3.6 32.1 - - + -
153G LEU* 4.3 2.7 - - + -
169G VAL* 4.1 7.4 - - + -
170G TYR 3.6 6.1 - - - +
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Residues in contact with PHE 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ARG* 4.1 30.3 - - + -
67G ILE* 1.3 75.1 - - - +
69G ILE* 1.3 61.5 + - - +
70G GLU 4.1 0.7 - - - -
140G GLU* 3.6 23.3 - - + -
141G ARG 3.4 4.5 - - - -
142G SER* 3.8 22.7 - - - -
168G ARG 3.6 1.0 - - - +
169G VAL* 3.2 5.4 - - - +
170G TYR* 2.8 65.1 + + + +
171G TYR* 4.6 1.1 - - - -
172G LYS* 3.5 50.0 - - + -
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Residues in contact with ILE 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G ILE* 4.0 15.0 - - + -
68G PHE* 1.3 79.4 - - - +
70G GLU* 1.3 59.4 + - - +
71G LEU* 3.8 25.9 + - + +
94G LEU* 4.2 26.6 - - + +
115G ILE* 4.8 2.5 - - + -
139G GLU 3.7 1.6 - - - +
140G GLU* 3.2 5.3 - - - +
141G ARG* 2.7 36.5 + - - +
143G VAL* 4.0 27.4 - - + -
153G LEU* 3.8 44.9 - - + -
167G VAL* 4.7 1.3 - - + -
168G ARG 3.5 3.8 - - - +
169G VAL* 4.5 6.1 - - + +
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Residues in contact with GLU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GLU* 4.2 16.6 - - - +
68G PHE 4.1 0.4 - - - -
69G ILE* 1.3 74.8 - - - +
71G LEU* 1.3 66.2 + - - +
72G LYS* 3.5 22.2 - - - +
138G VAL* 3.7 29.1 - - + +
139G GLU 3.4 5.4 - - - +
140G GLU* 3.9 22.5 - - + +
166G SER* 3.8 3.5 + - - +
167G VAL* 3.3 4.9 + - - -
168G ARG* 2.8 64.8 + - + +
170G TYR* 4.9 4.0 - - + -
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Residues in contact with LEU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ILE* 3.8 20.2 - - + +
70G GLU* 1.3 81.4 - - - +
72G LYS* 1.3 61.9 + - - +
73G PHE* 4.0 11.7 - - + -
92G PHE* 4.0 28.3 - - + -
94G LEU* 4.5 8.5 - - + -
118G ILE* 4.0 24.2 - - + -
137G ASN 3.7 0.2 - - - +
138G VAL* 3.3 5.5 - - - +
139G GLU* 2.9 36.9 + - + +
155G PHE* 3.6 29.2 - - + -
164G LEU* 4.3 4.5 - - + -
166G SER 3.3 3.4 - - - +
167G VAL* 3.9 16.6 - - + -
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Residues in contact with LYS 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GLU* 5.1 9.6 + - - +
172C LYS* 4.3 30.3 - - - +
173C LYS 5.7 0.6 - - - +
174C CYS* 5.0 14.1 + - + +
70G GLU* 3.5 27.1 - - - +
71G LEU* 1.3 77.9 - - - +
73G PHE* 1.3 64.5 + - - +
136G LEU* 3.9 27.6 - - + -
137G ASN 3.0 6.7 - - - +
138G VAL* 4.1 23.3 - - + +
164G LEU* 3.7 2.6 - - - +
165G LEU* 2.8 26.2 + - + -
166G SER* 3.0 34.2 + - - +
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Residues in contact with PHE 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G LEU* 4.0 11.4 - - + -
72G LYS* 1.3 78.7 - - - +
74G THR* 1.4 61.7 + - - +
75G VAL* 3.6 31.2 - - + -
92G PHE* 3.7 23.3 - + + -
118G ILE* 3.5 20.6 - - + -
119G ALA 3.9 6.7 - - - -
120G PRO* 3.9 9.0 - - + -
135G LYS 3.8 0.2 - - - +
136G LEU* 3.5 6.5 - - - +
137G ASN* 2.8 64.8 + - + +
139G GLU* 3.7 30.3 - - + -
162G VAL* 4.6 1.1 - - + -
163G ALA 3.1 16.2 - - - +
164G LEU* 4.1 11.4 - - + -
165G LEU* 4.5 0.7 - - - +
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Residues in contact with THR 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G PHE* 1.4 73.1 - - - +
75G VAL* 1.3 70.8 + - - +
124G THR* 4.3 6.1 - - - +
134G VAL* 4.5 13.0 - - + -
135G LYS 3.4 28.9 - - - +
136G LEU* 4.4 10.3 - - + -
137G ASN* 4.2 1.1 - - - +
162G VAL* 3.4 4.9 - - - +
163G ALA* 2.9 41.0 + - - +
165G LEU* 4.9 1.8 - - + -
113H PRO* 2.8 26.9 + - - +
114H PHE* 4.4 10.8 - - + -
115H THR 6.2 0.4 - - - +
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Residues in contact with VAL 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G PHE* 3.6 28.7 - - + -
74G THR* 1.3 81.6 - - - +
76G ARG* 1.3 67.8 + - - +
89G LYS 5.1 1.3 - - - +
90G GLU* 3.8 26.7 - - - +
91G THR* 5.9 0.2 - - - -
92G PHE* 4.8 3.6 - - + -
120G PRO* 3.7 20.6 - - + -
122G GLU 4.9 0.2 + - - -
123G ILE* 3.7 18.6 - - + -
124G THR* 2.8 28.9 + - - -
137G ASN* 4.3 4.0 - - - +
160G ALA* 5.1 0.2 - - + -
161G CYS 3.4 10.3 - - - +
162G VAL* 3.9 16.4 - - + -
113H PRO* 5.1 1.3 - - - -
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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