Contacts of the strand formed by residues 98 - 104 (chain B) in PDB entry 4F1E
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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ILE* 4.2 4.5 - - + -
46A ASN* 3.7 20.9 - - + +
55A LYS* 3.9 4.3 - - - +
56A ILE 4.3 0.9 - - - -
75A TRP* 3.6 35.9 - - + +
73B ARG 4.9 0.7 - - - +
74B CYS* 3.8 22.9 - - + -
87B HIS* 4.0 7.7 - - + +
90B HIS* 3.6 20.2 - - + -
91B ASN* 2.9 36.6 + - - +
96B ASP* 3.4 16.6 - - - +
97B ASN* 1.3 79.9 - - - +
99B GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 4.3 3.8 - - - -
56A ILE 3.0 24.2 + - - +
57A VAL* 4.1 4.0 - - - -
75A TRP* 3.6 5.3 - - - -
73B ARG* 2.9 25.1 + - - +
87B HIS* 4.5 2.9 - - - -
98B VAL* 1.3 75.2 - - - +
100B PRO* 1.3 70.1 - - - +
201B FES 3.9 7.9 - - - -
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 4.4 1.8 - - - +
57A VAL* 3.4 25.6 - - + +
58A HIS 3.3 12.0 + - - -
70B VAL* 3.7 23.8 - - + -
71B TYR 3.2 15.9 - - - +
73B ARG* 3.2 18.8 + - + +
83B CYS* 3.8 19.7 - - + -
87B HIS* 3.8 22.0 - - + +
99B GLY* 1.3 84.8 - - - +
101B LEU* 1.3 60.2 + - - +
102B ILE* 4.9 2.9 - - + -
201B FES 3.8 4.5 - - - -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A HIS* 3.4 30.1 - - + +
60A PHE* 3.9 22.2 - - + -
71A TYR* 3.4 48.0 - - + -
81A PRO* 5.0 0.2 - - + -
101A LEU* 3.8 17.7 - - + -
69B ALA 3.7 1.2 - - - +
70B VAL* 3.5 1.6 - - - -
71B TYR* 2.7 42.5 + - + +
73B ARG* 3.8 23.7 - - + +
100B PRO* 1.3 72.7 - - - +
102B ILE* 1.3 60.2 + - - +
103B ILE* 3.9 11.0 - - + -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL* 3.9 16.6 - - + -
58A HIS 2.7 13.6 + - - +
59A ALA* 3.2 10.7 - - + -
60A PHE 2.8 31.2 + - - -
68B LYS* 3.7 28.7 - - + -
69B ALA 3.4 7.2 - - - +
70B VAL* 3.9 23.1 - - + -
100B PRO* 4.9 2.7 - - + -
101B LEU* 1.3 75.6 - - - +
103B ILE* 1.3 66.3 + - - +
104B LYS* 4.6 9.6 - - + -
63M GLU 5.1 0.9 - - - +
64M ASP* 3.5 39.9 - - + +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 3.5 13.5 - - + +
62A MET* 3.7 20.6 - - + +
65A LEU* 3.9 17.5 - - + -
71A TYR* 3.4 38.4 - - + +
103A ILE* 4.6 3.1 - - + -
65B LEU* 3.5 26.0 - - + -
68B LYS* 3.3 1.4 - - - +
69B ALA* 2.8 37.8 + - - +
71B TYR* 3.9 22.4 - - + -
101B LEU* 3.9 14.1 - - + -
102B ILE* 1.3 81.8 - - - +
104B LYS* 1.3 62.1 + - - +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA* 5.2 1.1 - - + -
60A PHE 2.9 11.8 + - - +
61A ASP* 2.9 35.2 + - - +
62A MET* 2.8 36.4 + - - +
67B GLY 3.4 13.0 - - - +
68B LYS* 4.2 16.4 - - + +
102B ILE* 4.6 11.7 - - + -
103B ILE* 1.3 75.9 - - - +
105B LYS* 1.4 65.5 + - - +
106B LYS 4.7 5.9 + - - -
59M ALA* 2.7 30.1 + - - +
60M PHE* 3.8 23.3 - - - +
64M ASP* 4.2 14.4 - - - +
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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