Contacts of the strand formed by residues 94 - 102 (chain G) in PDB entry 4PKI
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 94 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G ARG* 3.7 3.3 - - - +
73G VAL* 3.1 28.3 + - + +
93G ASP* 1.3 74.6 - - - +
95G TYR* 1.3 64.0 + - - +
115G TRP 3.3 10.5 - - - +
116G LEU* 3.9 16.4 - - + +
120G CYS* 4.1 3.5 - - - +
124G GLU* 3.5 41.3 - - + +
125G SER 4.1 0.4 - - - +
128G ALA* 4.0 4.0 - - + -
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Residues in contact with TYR 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ILE* 3.9 14.4 - - + -
71G TRP 3.3 16.4 - - - +
72G ARG* 3.6 25.0 - - + +
73G VAL 4.7 0.4 - - - +
81G VAL* 3.9 15.0 - - + -
88G ASP 3.9 4.9 + - - -
89G PHE* 3.5 31.4 - + + -
90G PHE* 2.9 56.9 + - - +
93G ASP* 3.9 9.0 - - + -
94G ALA* 1.3 78.4 - - - +
96G VAL* 1.3 66.9 + - - +
97G ILE* 3.9 16.2 - - + -
114G TYR* 3.2 6.8 - - - +
115G TRP* 2.9 41.1 + + + +
128G ALA* 4.3 2.1 - - - +
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Residues in contact with VAL 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ILE* 3.5 1.4 - - - -
71G TRP* 2.8 46.1 + - + +
73G VAL* 4.9 1.8 - - + -
78G LEU* 3.9 27.6 - - + -
95G TYR* 1.3 77.8 - - - +
97G ILE* 1.3 62.4 + - - +
112G LEU* 4.0 13.5 - - + -
113G HIS 3.6 3.6 - - - +
114G TYR* 4.6 0.2 - - + -
128G ALA* 3.9 30.5 - - + +
131G PHE* 4.5 3.6 - - + -
132G THR* 4.1 12.3 - - - +
135G LEU* 4.0 26.7 - - + -
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Residues in contact with ILE 97 (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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68G LEU* 3.6 28.9 - - + -
69G GLN 3.4 6.5 - - - +
70G ILE* 4.0 22.0 - - + -
89G PHE* 4.1 5.4 - - + -
95G TYR* 3.9 21.3 - - + -
96G VAL* 1.3 80.0 - - - +
98G LEU* 1.3 63.6 + - - +
111G ASP 3.6 1.0 - - - +
112G LEU* 3.4 8.3 - - - +
113G HIS* 2.7 48.2 + - + +
115G TRP* 4.0 9.0 - - + -
157G PHE* 3.7 38.1 - - + -
160G TYR* 4.5 8.7 - - + -
161G PHE* 5.0 1.1 - - + -
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Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ALA* 4.1 13.5 - - + -
63G GLY* 3.7 21.5 - - - +
67G GLY 3.7 0.9 - - - +
68G LEU* 3.6 7.3 - - - -
69G GLN* 3.0 51.7 + - - +
71G TRP* 3.9 18.1 - - + -
97G ILE* 1.3 72.5 - - - +
99G LYS* 1.3 60.6 + - - +
100G THR* 3.7 7.4 + - - +
110G TYR* 4.0 27.6 - - + -
111G ASP 3.5 11.9 - - - +
112G LEU* 3.9 20.4 - - + -
135G LEU* 4.6 3.4 - - + -
139G LEU* 4.3 13.0 - - + -
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Residues in contact with LYS 99 (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 GLY* 3.5 23.1 - - - +
68G LEU* 3.8 17.9 - - + +
97G ILE* 4.1 1.6 - - - +
98G LEU* 1.3 71.0 - - - +
100G THR* 1.3 68.8 + - - +
101G VAL* 3.9 23.2 + - + +
109G GLN 3.4 4.7 - - - +
110G TYR* 3.5 1.4 - - - -
111G ASP* 2.9 36.6 + - + +
160G TYR* 3.4 50.9 - - + +
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Residues in contact with THR 100 (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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63G GLY* 3.4 21.4 - - - +
65G GLU 3.3 29.5 + - - +
66G PRO* 3.2 6.4 - - + +
67G GLY 2.8 38.2 + - - +
69G GLN* 4.2 3.3 + - - -
98G LEU* 3.7 6.8 + - - +
99G LYS* 1.3 75.5 - - - +
101G VAL* 1.3 63.2 + - - +
108G LEU* 3.6 32.3 - - + -
109G GLN 3.3 2.9 - - - +
110G TYR* 3.7 14.0 - - + -
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Residues in contact with VAL 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G PRO* 4.7 0.9 - - - -
99G LYS* 3.9 29.1 + - + +
100G THR* 1.3 77.9 - - - +
102G GLN* 1.3 73.1 + - - +
103G LEU* 4.1 13.5 - - + -
108G LEU* 3.4 3.6 - - - -
109G GLN* 2.6 63.6 + - + +
111G ASP* 5.7 1.1 - - - +
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Residues in contact with GLN 102 (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 PRO* 3.6 32.5 - - + +
101G VAL* 1.3 79.1 - - - +
103G LEU* 1.3 78.5 + - - +
104G ARG* 4.5 4.9 + - - -
106G GLY* 3.5 25.3 + - - -
108G LEU* 3.5 26.5 - - + +
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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