Contacts of the strand formed by residues 3 - 10 (chain B) in PDB entry 1P7L
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 HIS 3 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A MET* 3.7 36.8 - - + +
312A VAL 5.7 1.8 - - - +
1B ALA* 4.2 5.8 + - - +
2B LYS* 1.3 79.6 - - - +
4B LEU* 1.3 73.0 + - - +
5B PHE* 4.5 6.6 - - + +
172B TYR* 2.8 72.7 + + + +
175B GLY* 5.4 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLN* 4.3 2.3 + - - -
308A THR 5.0 9.0 - - - +
309A SER* 4.6 17.3 + - - -
310A ILE 4.2 13.7 + - - +
311A MET* 3.1 30.5 - - - +
2B LYS* 6.1 2.2 - - + -
3B HIS* 1.3 84.4 - - - +
5B PHE* 1.3 59.8 + - - +
6B THR 4.3 0.2 - - - -
169B THR* 4.6 6.7 - - - +
170B PHE 3.3 16.8 - - - +
171B GLN* 3.5 24.2 - - + -
181B ASP* 3.9 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 5.2 0.2 - - + -
123A PHE* 4.1 2.2 - + - -
256A ARG* 3.4 28.9 - - - -
297A GLN* 3.7 21.8 - - - +
311A MET* 4.8 4.9 - - - -
3B HIS* 4.2 9.7 + - + +
4B LEU* 1.3 74.3 - - - +
6B THR* 1.3 69.3 + - - +
7B SER* 3.4 22.6 + - - -
137B PRO* 3.9 18.8 - - + -
168B VAL 4.2 0.5 - - - +
169B THR* 3.5 1.2 - - - -
170B PHE* 3.0 33.2 + - - +
172B TYR* 4.1 18.4 - - + -
252B GLY 4.0 2.5 - - - -
253B GLY 3.4 9.0 - - - -
254B MET* 3.2 47.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.0 28.9 - - + +
297A GLN* 3.3 9.7 + - - +
299A SER* 3.6 21.8 - - - +
309A SER* 2.5 35.7 + - - -
5B PHE* 1.3 79.3 - - - +
7B SER* 1.3 68.3 + - - +
167B GLN* 3.6 22.2 - - + -
168B VAL 3.3 6.1 - - - +
169B THR* 3.3 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.2 4.5 - - - -
5B PHE* 3.4 13.2 + - - -
6B THR* 1.3 72.5 - - - +
8B GLU* 1.3 64.9 + - - +
137B PRO* 3.6 33.6 - - - +
138B ILE* 4.0 3.8 + - - -
141B ALA* 4.7 2.7 - - - -
167B GLN* 3.4 5.6 - - - +
168B VAL 3.1 30.4 + - - +
251B TYR 4.5 0.9 + - - -
252B GLY* 2.5 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.5 28.0 + - - +
120A GLY* 4.2 9.2 - - - -
121A LEU* 3.8 18.1 + - + +
258A GLY 4.0 15.2 - - - +
259A GLY* 5.7 0.5 - - - -
7B SER* 1.3 78.8 - - - +
9B SER* 1.3 65.1 + - - +
10B VAL* 5.1 3.1 - - - +
138B ILE* 3.7 10.4 - - - +
141B ALA* 3.9 6.1 - - - -
165B LYS* 4.2 10.0 + - - -
166B SER 3.2 12.8 - - - +
167B GLN* 4.1 8.3 - - - +
245B LYS* 5.2 2.1 - - - -
247B ILE* 6.5 0.9 - - + -
248B VAL* 3.5 31.1 - - + +
252B GLY* 4.9 1.9 + - - -
484B ANP 5.5 0.2 + - - -
487B MG 3.7 15.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 4.3 1.6 + - - -
8B GLU* 1.3 75.9 - - - +
10B VAL* 1.3 73.3 + - - +
141B ALA* 3.5 32.1 - - - -
142B HIS* 2.5 38.4 + - - -
145B VAL* 4.0 5.9 - - - +
165B LYS* 3.5 1.6 - - - +
166B SER* 2.7 31.4 + - - +
248B VAL* 4.1 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 5.1 3.4 - - - +
9B SER* 1.3 85.4 + - - +
11B SER* 1.3 62.2 - - - +
14B HIS* 3.8 24.0 - - + -
17B LYS* 3.9 22.4 - - + +
142B HIS* 6.0 0.2 - - - -
145B VAL* 3.6 12.7 - - - +
164B ALA 3.6 4.0 - - - -
165B LYS* 3.3 25.8 - - + -
245B LYS* 3.8 39.7 - - + -
248B VAL* 4.3 8.7 - - + +
357B TYR* 4.2 9.4 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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