Contacts of the strand formed by residues 97 - 107 (chain A) in PDB entry 3VF1
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 SER 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS* 5.5 1.8 - - - -
88A GLU* 3.6 24.4 + - - -
89A LYS 3.3 8.3 - - - -
90A ILE* 3.7 9.0 - - - +
96A PHE* 1.3 70.6 - - - +
98A ASN* 1.3 66.1 + - - +
99A LYS* 4.4 1.3 + - - +
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Residues in contact with ASN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 5.5 3.0 + - - -
88A GLU* 3.5 1.7 - - - +
89A LYS* 2.9 34.5 + - + +
90A ILE* 5.8 0.2 - - - -
91A ASP* 3.3 32.1 + - - +
96A PHE* 3.9 13.9 + - - +
97A SER* 1.3 82.2 - - - +
99A LYS* 1.3 63.3 + - - +
100A TYR* 3.6 32.7 + - + +
672B HIS* 5.7 1.6 + - - -
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE* 4.4 21.1 - - + -
87A ILE 3.7 3.8 - - - -
88A GLU* 3.8 35.0 - - + -
97A SER 4.4 1.3 + - - +
98A ASN* 1.3 75.4 - - - +
100A TYR* 1.3 65.4 + - - +
101A ILE* 4.0 12.4 + - + +
116A GLU* 5.2 1.4 - - - +
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY 3.9 4.3 + - - -
63A GLU* 3.3 39.2 + - + +
64A ILE* 3.3 47.3 - - + -
85A VAL 3.5 0.5 - - - +
87A ILE 3.0 30.3 + - - +
89A LYS* 3.9 16.5 + - + +
91A ASP* 5.8 2.3 - - - +
98A ASN* 3.6 39.3 + - + +
99A LYS* 1.3 76.7 - - - +
101A ILE* 1.3 63.5 + - - +
102A PHE* 3.0 35.4 - - + -
116A GLU* 4.4 12.3 - - + -
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 4.1 28.5 - - + +
85A VAL 3.6 4.0 - - - +
86A ILE* 3.6 36.1 - - + -
99A LYS* 4.0 15.4 + - + +
100A TYR* 1.3 72.6 - - - +
102A PHE* 1.3 63.4 + - - +
103A PRO* 3.7 11.4 - - + -
116A GLU* 3.5 15.7 + - - +
117A GLY* 3.1 24.2 + - - -
632A GLY* 6.5 1.3 - - - -
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.5 27.8 - - + -
66A MET* 3.7 18.6 - - - -
67A ILE* 3.6 27.6 - - + -
84A LYS* 3.3 3.6 - - - -
85A VAL* 2.8 39.3 + - + +
87A ILE* 3.8 19.3 - - + -
100A TYR* 3.0 45.5 - - + -
101A ILE* 1.3 73.2 - - - +
103A PRO* 1.3 67.0 - - - +
104A CYS* 3.2 6.8 + - - +
114A VAL* 3.6 15.5 - - + -
115A TYR 3.3 23.3 - - - +
116A GLU* 3.7 14.4 - - + -
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Residues in contact with PRO 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA 4.3 0.7 - - - +
84A LYS* 4.0 11.0 - - + -
101A ILE* 3.5 19.3 - - + +
102A PHE* 1.3 80.7 - - - +
104A CYS* 1.3 60.3 + - - +
105A TYR* 4.4 3.8 - - + -
114A VAL* 3.4 13.0 - - - +
115A TYR 4.2 3.7 - - - +
116A GLU 4.4 0.2 - - - -
117A GLY* 3.7 19.1 - - - +
400A LYS* 5.2 2.5 + - - +
629A ASN 3.8 20.4 - - - +
630A LEU* 3.6 37.6 - - + +
631A PHE 5.1 3.8 - - - +
632A GLY* 5.4 0.7 - - - -
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Residues in contact with CYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 5.1 3.1 - - - -
82A ILE* 3.5 19.3 - - + +
83A ALA 2.9 16.7 + - - +
84A LYS* 4.3 2.2 - - - -
85A VAL* 5.3 2.5 - - + +
102A PHE 3.2 7.6 + - - +
103A PRO* 1.3 75.1 - - - +
105A TYR* 1.3 77.7 + - - +
106A ARG* 3.4 26.8 + - - +
112A LEU* 3.4 32.5 - - - -
114A VAL* 3.9 15.0 - - + -
403A TYR* 6.0 0.9 - - - -
630A LEU* 4.2 6.4 - - - +
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Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.8 28.8 + + - +
82A ILE 2.8 19.3 + - - -
83A ALA* 2.9 40.8 + - + +
84A LYS* 4.5 16.1 + - + +
103A PRO* 4.4 4.0 - - + -
104A CYS* 1.3 80.3 - - - +
106A ARG* 1.3 65.7 + - - +
173A ASP* 5.9 0.2 - - - +
403A TYR* 3.9 19.6 + + + +
407A LYS* 6.3 0.2 - - - +
627A ALA 3.5 15.6 + - - -
628A ASP* 3.4 53.8 - - + +
629A ASN 3.7 12.4 + - - -
630A LEU* 3.6 19.3 - - + -
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A TRP 3.7 1.0 - - - +
81A TYR* 3.6 8.9 - - - -
82A ILE* 3.1 25.8 + - - +
104A CYS* 3.4 21.8 + - - +
105A TYR* 1.3 86.2 - - - +
107A TRP* 1.3 64.4 + - - +
108A VAL* 3.9 0.3 + - - +
112A LEU* 3.7 42.0 - - + +
114A VAL* 6.1 0.2 - - + -
138A GLU* 4.5 7.7 + - - -
142A ASN* 5.5 3.4 + - - +
173A ASP* 3.5 32.6 + - - +
389A TRP* 3.9 23.9 - - - -
394A SER* 4.1 17.4 + - - -
399A TRP* 3.7 26.7 - - - +
403A TYR* 4.8 10.1 + - - -
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Residues in contact with TRP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.6 28.3 - - + +
13A ARG* 3.8 11.4 - - - -
14A GLY* 3.3 32.8 - - - -
79A ASP* 3.2 40.4 - - + -
80A TRP 3.6 3.8 - - - -
81A TYR* 3.6 31.9 - + + -
106A ARG* 1.3 79.3 - - - +
108A VAL* 1.3 65.3 + - - +
109A ILE* 3.8 23.7 - - + +
112A LEU* 4.3 6.4 - - - +
172A LYS* 3.7 49.4 + - + +
173A ASP* 3.0 28.1 + - - +
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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