Contacts of the strand formed by residues 94 - 101 (chain S) in PDB entry 4IOA
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 94 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48S THR* 3.4 28.0 - - - +
49S THR* 3.7 20.0 - - + -
65S LEU* 4.9 11.9 - - + -
91S PRO* 5.6 3.1 - - + -
92S VAL* 3.7 18.2 - - + +
93S GLU* 1.3 75.5 - - - +
95S SER* 1.4 62.6 + - - +
96S VAL* 3.8 4.3 - - + -
120S LEU 3.0 13.9 - - - +
121S GLN* 3.4 5.2 - - - -
122S ILE* 3.1 30.9 + - + +
125S PRO* 4.4 8.1 - - + -
130S ILE* 4.2 20.6 - - + -
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Residues in contact with SER 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J TYR* 5.8 2.9 - - - -
48S THR* 3.1 30.2 + - - -
49S THR* 3.3 11.3 - - - +
94S VAL* 1.4 71.3 - - - +
96S VAL* 1.3 60.5 + - - +
97S PRO* 4.1 1.0 - - - +
119S ASN* 3.4 28.2 + - - +
120S LEU 3.3 7.6 - - - -
121S GLN* 3.6 18.5 + - - +
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Residues in contact with VAL 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S THR* 3.6 13.0 - - + -
94S VAL* 3.8 4.3 - - + +
95S SER* 1.3 73.9 - - - +
97S PRO* 1.4 70.9 - - + +
98S VAL* 3.3 5.0 + - - +
119S ASN* 4.2 1.8 - - - -
120S LEU* 2.8 38.8 + - + +
122S ILE* 3.6 35.9 - - + -
131S PRO* 3.4 20.2 - - + +
133S GLU 3.4 31.2 - - - +
134S LEU* 3.8 17.4 - - + +
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Residues in contact with PRO 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J TYR* 5.7 2.2 - - - +
47S SER* 6.0 1.8 - - - +
48S THR* 5.7 0.4 - - - +
49S THR* 3.6 19.1 - - - +
95S SER 4.1 3.1 - - - +
96S VAL* 1.4 83.8 - - + +
98S VAL* 1.3 62.2 + - - +
99S HIS* 3.5 23.0 + - + -
118S HIS 3.6 2.9 - - - +
119S ASN* 3.5 21.5 - - - +
132S GLN 3.9 15.5 - - - +
133S GLU* 4.2 3.6 - - + -
134S LEU* 3.1 27.1 + - - +
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Residues in contact with VAL 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96S VAL 3.9 10.8 - - - +
97S PRO* 1.3 70.7 - - - +
99S HIS* 1.3 71.7 + - - +
115S ILE* 4.0 21.2 - - + +
117S VAL 3.5 22.9 - - - +
118S HIS* 3.3 8.2 + - - +
120S LEU* 4.1 22.4 - - + +
134S LEU* 3.7 16.6 - - + +
136S VAL* 4.6 13.7 - - + -
152S ILE* 5.8 0.4 - - + -
168S VAL* 3.8 26.7 - - + -
169S VAL* 5.0 7.0 - - + -
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Residues in contact with HIS 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97S PRO* 3.5 32.3 + - + +
98S VAL* 1.3 83.7 - - - +
100S THR* 1.3 63.8 + - - +
115S ILE* 5.9 2.5 - - - -
133S GLU* 4.2 18.0 + - + +
134S LEU 3.1 8.9 + - - +
135S VAL* 4.0 21.3 - - + -
136S VAL* 3.1 29.6 + - - +
169S VAL* 5.8 0.7 - - - +
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Residues in contact with THR 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99S HIS* 1.3 78.3 + - - +
101S THR* 1.4 71.6 + - - +
102S GLY 4.8 2.5 - - - +
113S VAL* 4.0 20.7 - - + +
115S ILE* 5.2 9.0 - - + -
135S VAL* 5.3 0.2 - - - +
136S VAL* 3.5 3.6 + - - +
138S VAL* 3.4 37.1 - - + +
169S VAL* 4.2 8.3 - - - +
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Residues in contact with THR 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100S THR* 1.4 79.1 - - - +
102S GLY* 1.3 67.3 + - - +
135S VAL* 3.4 39.4 - - + +
136S VAL 3.3 3.6 + - - -
137S ASP* 3.5 27.1 + - - +
138S VAL 3.3 19.9 + - - -
139S THR* 4.2 0.3 + - - -
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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