Contacts of the strand formed by residues 2 - 8 (chain A) in PDB entry 1L8F
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 ASN 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ALA* 1.3 82.8 + - - +
3A GLY* 1.3 58.7 + - - +
4A GLN* 5.3 2.2 - - - +
94A THR* 5.4 2.8 + - - +
117A ASN* 3.2 24.3 + - - +
181A PHE 3.3 8.8 + - - +
182A THR* 3.2 26.6 - - - +
183A PHE* 4.0 5.2 - - - -
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Residues in contact with GLY 3 (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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2A ASN* 1.3 76.3 - - - +
4A GLN* 1.3 72.6 + - - +
117A ASN* 3.1 17.5 - - - -
180A SER* 3.6 7.1 - - - -
181A PHE* 2.9 44.0 + - - -
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Residues in contact with GLN 4 (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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2A ASN* 5.3 1.6 - - - +
3A GLY* 1.3 85.1 + - - +
5A SER* 1.3 61.8 + - - +
6A THR* 5.6 1.3 - - + -
116A SER* 3.4 22.3 + - - -
117A ASN 2.9 22.5 + - - +
118A HIS* 3.0 12.9 - - + +
119A PHE 2.9 23.9 + - - -
178A ASN 5.7 1.3 - - - +
180A SER* 4.7 8.0 - - - +
181A PHE* 3.3 5.2 - - - -
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Residues in contact with SER 5 (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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4A GLN* 1.3 77.5 - - - +
6A THR* 1.3 77.1 + - - +
93A PHE* 4.8 1.3 - - - -
118A HIS* 6.0 0.2 - - - -
119A PHE 3.1 9.4 - - - -
121A LEU* 4.8 13.2 - - - +
173A PHE* 5.2 0.2 - - - -
178A ASN* 3.2 21.1 + - - +
179A PRO* 2.6 47.2 + - - +
181A PHE* 3.5 15.9 - - - -
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Residues in contact with THR 6 (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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4A GLN* 5.6 2.2 - - + -
5A SER* 1.3 86.8 + - - +
7A ARG* 1.3 65.8 + - - +
118A HIS* 6.1 2.9 - - + +
119A PHE 3.0 3.2 + - - -
120A ASP* 2.9 32.5 + - - +
121A LEU* 2.9 28.3 + - - +
178A ASN* 3.3 21.5 - - - +
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Residues in contact with ARG 7 (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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6A THR* 1.3 82.2 + - - +
8A TYR* 1.3 67.8 + - - +
121A LEU 3.4 6.1 - - - +
123A ILE* 3.9 21.5 - - + -
126A GLY* 3.3 24.8 - - - +
127A GLY* 4.5 0.3 - - - +
147A GLY* 2.9 42.4 + - - -
149A ILE 4.9 0.4 + - - -
169A ARG* 3.5 35.7 - - - +
173A PHE* 5.8 3.4 - - + -
175A ASN* 5.3 1.1 - - - -
176A ALA 4.3 7.0 + - - -
177A ASP* 3.0 39.4 + - - +
178A ASN* 4.0 9.2 + - - +
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Residues in contact with TYR 8 (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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6A THR* 5.9 0.2 - - - +
7A ARG* 1.3 79.2 - - - +
9A TRP* 1.3 70.3 + - - +
10A ASP* 3.6 38.1 - - + -
14A PRO* 6.1 0.2 - - - +
73A ALA* 3.8 17.8 - - + +
109A SER* 4.1 12.3 + - - -
120A ASP* 3.3 35.7 - - + -
121A LEU 3.0 12.6 + - - -
122A ASN* 3.4 32.0 + - - -
123A ILE 2.8 26.9 + - - +
126A GLY* 4.0 5.3 + - - -
127A GLY 3.3 14.4 - - - +
128A VAL 5.1 2.9 - - - -
129A GLY* 5.7 1.6 - - - +
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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