Contacts of the strand formed by residues 71 - 76 (chain A) in PDB entry 1H3F
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 LYS 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PRO* 4.5 9.3 - - + +
38A LEU 2.9 15.6 + - - +
39A THR* 3.4 8.8 - - - +
40A VAL* 2.7 33.9 + - - -
69A GLY 4.1 0.4 + - - -
70A HIS* 1.3 72.1 - - - +
72A VAL* 1.3 64.6 + - - +
73A VAL* 4.7 7.9 - - + -
120A PRO 3.6 18.9 + - - -
121A HIS* 3.8 19.1 - - - +
122A LEU* 3.8 8.1 - - - +
124A GLU* 2.8 45.2 + - - +
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Residues in contact with VAL 72 (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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40A VAL* 3.3 15.9 - - + +
62A MET* 3.4 47.6 - - + +
65A PHE* 5.3 1.3 - - + -
66A GLN* 3.7 29.2 - - + +
70A HIS 4.0 0.4 + - - +
71A LYS* 1.3 75.9 - - - +
73A VAL* 1.3 74.6 + - - +
74A LEU* 4.0 3.4 - - - +
116A LEU* 4.5 2.5 - - + -
122A LEU 3.0 13.7 + - - +
123A PHE* 3.3 17.7 - - + -
124A GLU 2.9 24.9 + - - -
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Residues in contact with VAL 73 (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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39A THR* 3.6 26.0 - - + -
40A VAL 2.8 10.9 + - - +
41A LYS* 3.7 1.6 - - - -
42A LEU 3.2 23.7 + - - +
71A LYS* 4.7 8.3 - - + +
72A VAL* 1.3 77.4 - - - +
74A LEU* 1.3 60.8 + - - +
75A ILE* 3.7 8.3 + - + +
124A GLU* 3.4 22.0 - - + +
126A ARG* 3.8 29.8 - - + +
186A ILE* 3.8 31.0 - - + -
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Residues in contact with LEU 74 (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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42A LEU* 3.5 29.8 - - + +
44A ALA* 4.6 5.8 - - + -
59A LEU* 5.5 0.4 - - + -
62A MET* 5.2 0.2 - - + -
72A VAL* 4.0 5.0 - - + -
73A VAL* 1.3 70.3 - - - +
75A ILE* 1.3 61.5 + - - +
76A ILE* 4.6 3.8 - - + -
108A TYR* 3.7 43.7 - - + +
109A VAL* 4.8 3.8 - - + -
112A ALA* 4.3 11.7 - - + -
116A LEU* 4.6 5.8 - - + -
123A PHE* 3.8 36.1 - - + -
124A GLU 2.8 9.7 + - - +
125A LEU* 3.5 17.3 - - + +
126A ARG 2.9 26.7 + - - +
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Residues in contact with ILE 75 (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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41A LYS* 3.8 35.0 - - + -
42A LEU 2.9 12.2 + - - +
43A GLY* 3.3 5.3 - - - -
44A ALA* 3.0 26.2 + - - -
73A VAL* 4.2 16.8 - - + +
74A LEU* 1.3 74.5 - - - +
76A ILE* 1.3 65.1 + - - +
77A GLY* 3.4 0.7 + - - -
126A ARG* 3.3 8.7 - - + +
128A ASN* 3.9 35.7 - - + +
131A TRP* 4.1 7.2 - - + -
182A ASP* 3.9 18.2 - - + +
186A ILE* 4.0 21.8 - - + -
1433A TYE 4.2 1.5 - - - +
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Residues in contact with ILE 76 (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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44A ALA* 3.7 6.3 - - + +
46A PRO* 3.3 29.6 - - + -
74A LEU* 4.6 4.5 - - + -
75A ILE* 1.3 74.3 - - - +
77A GLY* 1.3 57.3 + - - +
78A ASP* 3.0 13.0 + - + +
101A THR* 5.7 0.2 - - + -
105A ALA* 4.3 16.2 - - + -
108A TYR* 4.2 26.2 - - + -
109A VAL* 4.2 7.9 - - + -
125A LEU* 3.8 28.5 - - + -
126A ARG 2.7 11.7 + - - +
127A TYR* 3.4 32.9 - - + -
128A ASN* 3.1 21.8 + - - -
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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